That is the question.
Well all I can tell you are a few of my own thoughts on the two choices. The Megaton house does have a fridge, something noticeably missing from the TP suite.
No bathroom in either, a curious thing, especially in TP where the other luxery suites on the same floor all have them. In Megaton though everyone pretty much has free use of the public bathrooms so it's understandable there.
The bed in TP is much nicer, if that matters to anyone.
Megaton sees regular visits from caravans. TP, not so much. As in none. Hey, it's something to consider.
The only thing to really ask yourself is do you feel like playing a good character or a bad one?
I have at times found myself wishing there was a second way to attain the TP Tower suite, one that doesn't involve evaporating an otherwise fairly interesting town and all it's inhabitants. And without cheats.