I would recommend "La Pyramide", a nice but small hotel in the middle of the city. The owner who speaks Spanish, English, and German, can provide you any information. He will pick you up at the airport day or night, and take you to the airport from the hotel.Edited: 25 March 2012, 23:54
There's more flexibility in Granada, easy to get in and out of town. Less hustle and bustle.
However, really enjoyed my stay at La Pyramide Hotel (check out the reviews), which is a very peaceful place, walking distance to Hippos neighborhood.
We had a great dinner near La Pyramide at Restaurant Dona Haydee.
Donya Haydee is a great restaurant...I second Joshbash's recommendation for that place...has good typically Nicaraguan food.
Managua - you can 'see' (there isn't really a whole lot to see as in the traditional sense) the entire city's sites in <1 day. I'd recommend getting in touch with Nica Adventures - they can set you up with a brilliant tour guide + driver at a reasonable rate.
The hotel I'd recommend is Camino Real - it certainly isn't boutiquey like La Pyramide nor is it in city centre. It does however, provide a nice respite from the world just beyond its perimeter. It has a nice pool, great buffet breakfast, tennis courts etc.
Also, as the others have echoed and I shall also, you really don't need to spend much time in Managua - unless business or some compelling reason keeps you there. You could spend a day/night then I'd go to another town. Granada is more in line with what you'd expect a central American town to look like.
By car, it took about 20 minutes.
The only thing they missed IMO is the Malecon and Puerto Salvador Allende. This is all re-done and very nice place to relax by the lake and enjoy something to eat or drink.
Gracias Mike..... I checked our your website and I'll be shooting you email in a bit