how would you hide the fuel cycle in the middle of DC?
Well, it helps that the pentagon isn't in the middle of DC--it's across the river in Virginia
There has been a TON of development in VA (like all the other suburbs of DC) in the last several decades, so during the time of interest there would be a lot more undeveloped land to work with than there is now, even within a few km of the pentagon.
The DC metro area is a major population center and as such requires a lot of infrastructure. For a sense of scale, there are multiple five to eight foot diameter water mains serving the region today, although I'm not sure what the growth curve of the area around the pentagon has been like to say specifically how that translates to the cold war era. The Metro (train) system was first built in the 70s, though, and that sort of project could absolutely provide cover for a lot of clandestine construction. I would expect the pentagon to already have its own power plant, at least for steam for heating/hot water given the age and size of the building, and I don't think anyone would bat an eye at an expansion of those systems. An on-campus power plant also gives you some cover for waste heat, although probably nowhere near what you'd need for a nuke plant.
The Potomac river is only about 24ft deep, so I don't think you could hide gas discharge very well in that little depth, plus there were serious pollution issues with the river that weren't addressed until the 70s/80s which could have complicated the effort. Like foaming from protein content in the water, the gas bubbles liberating all kinds of unpleasant odors, and possible interaction with the local flora/fauna and bacterial/algal loads. As far as heat, the Potomac discharges about 10,810 cu.ft/s or about 306m^3/s, so back-of-the-envelope that's a heat capacity of about 1.28GJ/°C, if you could somehow get sufficient mixing. That would be a serious plumbing challenge though and would be hard to disguise.