We visit London quite a bit and were last there this summer. For planning, keep in mind, the Tower closes around 4-5pm, so if planning make sure you get there ASAP. Should be able to zip thru in 2 hours or so.
As for the London Eye, that closes latest of all the attractions, so pre-book the tix online for whatever is the latest ressie you can do. That takes 35 min for 1 revolution plus ~30-45 min wait depending on how long the line.
That leaves you a few hours in the middle, if you don't mind spending a bit of $$ to get to see a ton of places, I'd reccommend doing the Original Bus Tour or Big Bus Company tour...they have 2-3 different routes each, a loop around the major points of interest in the city with commentary and chance to hop on hop off as you wish. Even the biggest of the loops is only 3 hours, and there are stops at Tower of London & London Eye so you can use it as your transportation too. Hop off at Westminster, walk around to see Big Ben, Parlaiment, etc. There's a Tessco and various other places to grab a quick bite, then you can walk across the bridge to the London Eye. FYI it is awesome at night! HTH & PM if you need anything else!