BOYS town, the orphanage hailed by House Speaker Newt Gingrich as an alternative to welfare, itself receives what some deride as welfare: farm-subsidy payments. So do a children's hospital in Texas, an Illinois nursing home, and the Reorganized Church of Jesus Christ of Latter Day Saints (RLDS), headquartered in Independence, Mo. These are among the top recipients of $48 million in farm subsides paid to 2,266 churches and charities since 1985. Though that's just a few grains of corn out of the total farm-subsidy silo, it shows the extent to which federal aid, intended to help American agriculture, has been flowing out to other kinds of organizations. Indeed, critics like to point out that traditional family farms are far from the only entities receiving aid: Large urban landowners, agribusiness corporations, and general partnerships also account for hefty slices of a subsidy pie that has totaled $109 billion over 10 years. They will help fuel the bonfire of debate now just beginning in Congess over proposed cuts in agricultural subsidies. ''Taxpayers should be outraged'' about this system, claims Ken Cook, head of the Environmental Working Group and co-author of a study on farm subsidy recipients. Not so, say defenders of the status quo. John Ross, executive vice president of the American Society of Farm Managers and Rural Appraisers in Denver, says farm programs should be blind to ownership. Mr. Ross complains that critics focus on farm-income stabilization - the ''welfare'' function of the programs - while ignoring other functions like protecting the environment and assuring the country of abundant food at stable prices. Excluding categories of owners would work against those latter goals, he says. ''It really doesn't bother me'' that churches and charities share in subsidies, says Ross. ''The good work that they are doing relieves the taxpayer of a burden.'' America's tangled web of agricultural price supports and subsidies has long been a tempting target for budget-cutters. This year, big cuts may finally hit the farm-aid system, with the GOP drive to balance the federal budget outweighing the defensive efforts of rural lawmakers. As they stand now, US farm programs cost around $7 billion a year. In its fiscal 1996 budget resolution, Congress voted to slash up to $13.4 billion from agriculture over the next seven years. Congressional agriculture committees began meeting this week to draw up budget reduction details. Some members believe a $13.4 billion cut should only be the beginning. In the House, a coalition of urban and suburban lawmakers hopes to phase out farm aid entirely. As politics stands now, however, the leading agriculture reduction proposal is the so-called Freedom to Farm bill of House Agriculture Committee chairman Rep. Pat Roberts (R) of Kansas. UNDER the Freedom to Farm bill, subsidies would shrink year by year through 2002, but for the first time farmers need not do anything to earn them. They would have much greater freedom to plant whatever crops and as many acres as they wish, with the subsidies helping them make the transition to a market free of government interference. Any land that has been enrolled in farm programs for at least five years would be eligible for the strings-free handout, including land held by insurance companies, big-city dentists, universities, charities and other entities that do not fit the stereotype of the struggling family farmer. This summer Congress soundly defeated a means-test proposal that would have denied subsidies to entities with more than $100,000 in nonfarm income. The church/charity list was provided to the Monitor by the Environmental Working Group, which extracted it from US Department of Agriculture data obtained under the Freedom of Information Act. The list identified recipients only by city, state, and nine-digit zip code. Although relatively few subsidy dollars go to churches and charities, those nonprofit groups do not pay income taxes on the money. Ordinary farmers do. Farm ownership for some churches and charities far predates the start of federal subsidies in the 1930s. When Father Flanagan moved his home for boys outside of Omaha in 1917, he sought a farm as a source of food and a site for vocational training. The RLDS also trained young families in farming on land it bought in the late 1800s. Today Boys Town residents ''help out with light field duties'' but mostly focus on school, says spokesman John Melingagio. The charity's $541,000 in farm subsidies since 1985 pale in comparison with its budget this year alone of $94 million. Nor are the $616,000 in subsidies received by the RLDS significant to its operations. ''We're a church, not an agriculture organization,'' says RLDS spokesman Roger Yarrington. ''Our involvement in farming is more a factor of history and heritage ... than any intention in 1995 to be farm managers.'' Vastly more farmland is held by a church with which the RLDS is frequently confused, The Church of Jesus Christ of Latter-Day Saints based in Salt Lake City. The Mormon church never accepts subsidies, spokesman Don LeFevre says. ''We believe in doing it on our own.''