There are two Park Plaza hotels and a Premier Inn within a few blocks of Waterloo Station, among others. They're close to the south bank walkway, the London Eye, and via Westminster Bridge to many other sights. I've stayed at one of the Park Plazas and liked it fine. These are modern high-rise hotels without charm but with comfort and convenience. Waterloo is served by several tube lines to get you anywhere in London fast.
Another option might be to stay someplace near a Jubilee line tube station. This is the newest line, perhaps easier to navigate with luggage than some of the older lines. The stations are large and you'll find more escalators and elevators (lifts) than on other lines. It serves Waterloo as well as stations like Westminster, Green Park, Bond Street, and Baker Street, convenient for sightseeing.