Try the Holiday Inn on the Bay 619.232.3861
The Holiday Inn Harborside 619.239.9600
Ask for the Airline Crew Rate or Corporate Rate. Even if you aren't flying they will usually give you the better price.
Those 2 are "usually" airline friendly but can change depending on management. It's going to be tough getting a room bay the water for less than $100.
If you are looking for inexpensive rooms, check out Mission Valley or Hotel Circle. There are tons of cheap places to be found.....($40 - $80)
Hope this helps....
