There may be other seas in the world with water as clear and blue as the Aegean, but they are not the seas of Homer or of Aphrodite. And there may be other islands in the world as ruggedly beautiful as the Greek islands, but no others are so deeply and indelibly rooted in the history and myths of Western civilization.

That is why it is not scenic charm alone that makes a cruise of the Aegean and its hundreds of bleached islands the stirring feast for the eyes and the imagination that it is. To follow the course of Odysseus, sailing past olive-tree-covered hills, crumbling marble temples, and aquamarine coves, is to journey over millenniums as well as miles.

But while modern sailors of the Aegean may cherish the vision of Odysseus plying the waters in his wooden ship, they can choose from an array of vessels unimaginable to that ancient mariner. Among them are luxurious cruise ships, interisland ferries, the speedy hydrofoils called ''flying dolphins,'' chartered motor and sailing yachts that include a skipper and crew, and simple ''bareboats'' that can be chartered by those with sailing knowledge and skill.

On a recent visit to Greece I sampled two of these options, taking short cruises on a pair of vessels which shared a first name in common, but little else. The first was the SS Stella Solaris, an elegant liner which traveling companions and I joined on the island of Rhodes for a cruise to Samos and the ancient city of Ephesus in Turkey. The second was the Stella, a graceful white motor yacht that took us to the lovely and tranquil island of Poros, a mere three hours from the bustle of Athens and the nearby port of Piraeus.

Our acquaintance with the Stella Solaris came during the last three days of a week-long cruise of the eastern Mediterranean. Joining the ship when it called in at Rhodes, we boarded the impressive blue-and-white vessel that is the 18,000 -ton, eight-deck flagship of the Greek-owned Sun Line. After settling into our staterooms we joined the shore excursion tour of the old city of Rhodes.

Because I had always associated the Greek Islands with little whitewashed villages and classical ruins, the town of Rhodes came as a surprise: Once the domain of a largely Italian order of knights during the time of the Crusades, much of the old section of Rhodes looks like a stage setting for Camelot. Medieval fortifications guard a town, a meandering enclave of cobbled streets lined with golden stone buildings that recall the age of chivalry rather than of Alexander. There is even a deep, dry moat that adjoins the fortifications, a gorge filled with flowering pink oleander trees and graceful herds of brown and black deer.

As lovely as the medieval buildings are, the highlight of the tour is the collection of the ancient Greek art at the Archaeological Museum. Housed in the somewhat incongruous setting of the 15th-century Hospital of the Knights, the vaulted rooms and courtyards contain excavated treasures, some of which were unearthed during hotel construction on the island. Of these the most famous is the small, exquisite statue of a kneeling Aphrodite drying her long tangled hair after a bath. The perfectly intact marble treasure is believed to date from the 1st century BC.

Heading back toward the ship after the tour, I followed the curving Mandraki Harbor and tried to imagine what it looked like when the Colossus of Rhodes, the mountainous statue of a man built in the 3rd century BC and considered one of the seven wonders of the ancient world, guarded its entrance. Although the Colossus has long since toppled, the harbor is still impressively embellished, now with a lighthouse enclosed in a medieval fortress, three stone windmills, and a pair of columns that are each topped with a bronze deer.

When the Stella Solaris sailed out of Rhodes that evening, the tooth-edged city walls receding against the darkening sky, we had a chance to get to know the ship. Just as the staterooms are large and tastefully decorated, mostly in shades of green and rust, so are the library, lounges, theater, entertainment area, dining room, and even the wood-paneled discotheque. At dinner that evening attentive waiters brought plates of sweet local melon, heavenly Greek salad, and succulent roast lamb.

After a walk out on deck to admire the constellations casting a silvery light on Homer's ''wine dark'' sea, it was easy to be lulled to sleep by the gentle lapping of the Aegean. So lulling was it, in fact, that I awoke with a start the next morning to see the outline of a minaret outside my porthole; we were fast approaching our next port of call, the town of Kusadasi and the nearby ancient ruins of Ephesus.

Promptly at 8, we filed off the vessel into waiting buses for the short trip to Ephesus. As we wound above the chalk-white cliffs falling into the sea below, an occasional rug-draped camel and grove of silk trees told us that we had entered both another country and continent.

Even with the souvenir shops that flank both its entrance and its exit, and even with the throng of fellow tourists that one is obliged to view it with, Ephesus is an awesome sight to behold. Once a gleaming city of white marble that housed 300,000 inhabitants, it was one of the most resplendent capitals of the ancient Greek world, and later, an important center for the early spread of Christianity. Today, thanks largely to the diligent efforts of Turkish and Austrian archaeologists who have been excavating the site for the past 100 years , some of the most eloquent, hauntingly beautiful ruins that civilization has to offer have emerged from centuries of dust.

After the two-hour tour of Ephesus, the buses headed back to Kusadasi so that passengers could browse among the rugs and leather goods for sale in the lively port. Clutching a bag of what I considered to be the best buy of all - fresh, sweet Turkish figs - I boarded the Solaris at noon for the two-hour sailing to the Greek island of Samos.

Soon there was coastline on both sides of the ship, an indication that we had reached Samos, an island separated from Turkey by a mere mile of water. Entering into a crescent-shaped harbor, the ship dropped anchor in Pythagorion, a charming village of pleasant waterfront cafes, craft shops, and pastel-colored houses. After a bit of browsing in the shops, a friend and I enjoyed a swim at a rocky beach inhabited only by a few local sunbathers and a pair of black hens scratching gamely at the pebbled shore.

That night the ship pulled out of Pythagorion to sail to Piraeus, the final destination, which came all too soon the next morning. The letdown was not as great for us as it might have been, however, knowing as we did that we'd soon take to the sea again, this time in a chartered yacht.

A few days later we found, tucked in among the thousands of yachts moored at the docks of Piraeus, the sleek, white Stella, a 106-foot vessel that can easily accommodate 20 passengers and a crew of seven in its wood-paneled interior. Below deck are 10 staterooms; above is a large dining room, gallery, and sitting area. While most people who charter a yacht do so for at least a week or two, it is also possible to do as we did, and charter one for just a single unforgettable day.

Settling into rattan chairs on the rear deck of the Stella, we watched the pastel skyline of Piraeus grow smaller in the distance as we headed down the coast of the southern Greek mainland, the Peloponnesus, toward the island of Poros. In less than an hour the beautiful cliffs of the island of Aegina appeared to one side of us, their steep sides appearing rose violet in the luminous morning light. Above the cliffs the terrain is thickly dotted with groves of pine and conically shaped cypress trees, an occasional square white rooftop providing a contrast to the deep green.

As we neared Poros, the mountainous coast of the Peloponnesus came into view. Soon we were plying a narrow course just a quarter of a mile wide, with the mainland on one side and Poros on the other. When we came to a secluded cove known as Neorion, we dropped anchor about 150 yards from a stunning shoreline of rocky hillsides covered with olive trees and little umbrella-shaped pines. After lunch the Stella headed out from the cove to the town of Poros, docking at a harbor ringed by white houses with turquoise shutters and red-tiled roofs. Disembarking, we set out in all directions for a walk through the narrow, twisting streets with their hidden courtyards and blooming bougainvillea which cling to the sides of the whitewashed houses.

All too soon it was time to return to Piraeus, a journey that was made less sad by the fact that a deep salmon-colored sunset was well under way by the time we reached the twinkling lights of the port. Practical information:

Before planning your own Aegean odyssey, consider your priorities. If you want to get to know an individual island or archaeological site well, then the limited time that most cruise ships allow in ports of call may prove frustrating. Chartering your own boat and planning your own itinerary allows for the greatest flexibility. However, if what you want is an introduction to the islands and if you enjoy the amenities that a large vessel offers, then a cruise ship is for you.

From April to October of next year, Sun Line is offering a variety of Aegean and Mediterranean cruises that range from 3 to 15 days. Further information is available from Sun Line, One Rockefeller Plaza, New York, N.Y. 10022; (212) 397- 6400.

Chartering a yacht can be either one of the most economical or most expensive ways possible to tour the Greek islands. The Stella rents for $1,300 a day, a price that includes food, fuel, and crew. If the expense is shared among the 20 passengers that the yacht can carry, the cost per person is only $65 a day. More information is available from Regatta Yachts USA Inc., 123 East 54th Street, New York, N.Y. 10022; (212) 421-0389.

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