I found Budapest very beautiful on sunny days, while Prague is picturesque the entire year.

For cruising it depends on what you prefer. Some of the thermal baths in Budapest are very beautiful with Art Nouveau style and an Oriental touch, but they are usually mixed and cruising is more subtle.
The saunas in Prague are the usual gay saunas, but with too many rentboys. Prague has a fetish/cruising club called Alcatraz that is pretty modern, well maintained and the guys were smarter than in similar clubs in Western Europe. And it is not too touristy.

One thing to keep in mind is that Prague had been flooded in the 1990s with Western foreigners looking for cheap and young hustlers, and some hotels, bars and saunas still cater to this clientele. That, of course, influenced also the attitude of the gay locals towards gay tourists. Some may be looking for their money while others may look down on them or might be simply annoyed. Instead of aggressive cruising and expecting availability it's better to show interest and respect.