I've been to a few. The Golden Gate in Sheapheads Bay might be suitable for your needs. The price is about 60-90 for a short stay depending when you go. Some rooms are decent, others are in real bad shape. The Windjammer is even worse and I would avoid at all costs. There are some bad elements there. There's the Harbor off the belt pkwy. I haven't been there in a while, but from what I remember, it was fairly clean quiet but management is watchful. There is the Prince Hotel Bay Ridge.
Golden Gate: 60-90, just off belt pkwy, rooms vary but I always found it to be fairly clean, a little worn, but the bath was ok. No problems. Can get a little rowdy at night.
Harbor: 60-90, small motel, mostly couples not wanting to do it in the car. Also a bit worn but seems clean enough. Bathroom wasn't sparkling but clean.
Windjammer: Sleazy dive. Having problems. I would avoid
Prince hotel: In Bay Ridge, don't know if they even have short stays but supposedly very inexpensive. Never been there but heard it was ok
As I said, the prices vary. However, you can expect to pay over 50 for a 4 hour stay.
Good luck