The hotels in Kingston can be expensive. Waterfront hotels and hotels right downtown are only for those with large wallets. With cheaper ($100 a night average) hotels (read: EconoLodge) you risk sacrificing cleanliness. Going a bit further from downtown and the water is your best bet - you can stay in a nice hotel without breaking the bank.
The Holiday Inn Express is right off the 401 highway - which is really great for those travelling by car. It's on Division street, which is a straight shot to the start of downtown (an easy drive, but it would be a long way to walk). The price is extremely reasonable: for about $150 a night we got to stay in a very clean hotel with comfortable beds, a shower with good water pressure and temperature, a decent sized pool and hot tub, and a complimentary hot and cold breakfast that was available until 10 AM. When considering the amount of money we could have spent each day on breakfast (for three adults, we had been spending about $50 at other stages of our trip), the real value of this hotel becomes clear.
I highly recommend this hotel for any travellers to Kingston who will be driving during their stay.