You need a remote and base with addressable IR. There are several options including Harmony, Xantech, Next Generation and URC. Otherwise, you'll just have to spread the boxes out and angle them away from each other as much as you can.
If you would consider dumping cable, both DirecTV and Dish have addressable boxes. If want to keep cable, you can simply replace all your boxes with a cable card tuner in Windows Media Center and run 3 extenders all set to unique addresses. I don't know if Tivo has addressable boxes or not, but that's another option. At least with the Windows Media Center option, you save a lot of money in the long run since there are no DVR or box fees, but the upfront cost for all the equipment is a little steep ($100-$200 for a tuner, and $100 for each of your 3 other extenders).