There isn't much to choose from out by the Pentagonito. Frankly I'd recommend staying in San Isidro or Miraflores, and cabbing it back and forth.
Lately I've been staying at the Atton in San Isidro. It's not luxurious but it's new and has spacious rooms, a decent restaurant (I've only had breakfast there so far), a pool out back and a small but nicely done gym with saunas. Our corporate rate there is US$135 per night (VAT exempt) and for that I get a room with two double beds, not a big deal when I'm in Lima on business but will be great the next time I'm in Peru on vacation with my wife and two kids---we'll fit in a single room.