I stayed in the Holiday Inn on 26th between 6th and 7th Avenue. we found it to be a great location, staff couldn't do enough for us - very friendly. Very clean. I think it's a new enough one. Was about 600 for 5 nights for the two of us. We had a double bed each - very comfortable.
Stayed in the Hyatt at grand central station, great hotel, price was good too if i remember,also the bus from JFK drops you across the road from the hotel.
In my experience, the various buses from JFK to Manhattan are to be avoided unless you arrive at an especially quiet time for traffic. The train service is much better.