The Sidney Albert JCC in Albany does have a very safe and clean pool, but I have found the lap hours to be too limited for us because of swim team, water aerobics, etc. They do have very good morning swim hours.
If you join one of the Capital District YMCA's, you can use the facilities at any of them. The North Albany YMCA is more bare bones than the others, but it also tends to be not as crowded. I have only other ones I have visited are the Bethlehem & Guilderland YMCAs, but all three are very well maintained.
I have never been, but I know people downtown like the
Steuben Club. It is an old school type athletic club that is going through upgrades. I've heard a lot about the classes, not much about the pool. It is not open as late as the JCC and Y, though.