My third trip to Nicaragua was in May/June 2008. In Nicaragua, I've mainly stayed in Managua, the capital, but have traveled to Granada, Leon, San Juan del Sur, Rivas, Masaya, and a couple small towns (Diria for one). From Managua you can do day trips to many other locales. Go to the Masaya artisan market in the small town of Masaya, visit a volcano or two (Mombacho and Momotombo), and spend at least a day at the beach (San Juan del Sur, Pochomil, or Montelimar). Pochomil Beach is a more typical Nica beach, although Montelimar has the all inclusive Barcelos resort and San Juan del Sur has a lot of luxury hotels and is popular with tourists. I would suggest taking more than a day to visit Montelimar and San Juan, especially San Juan, which is quite a drive from the capital. If you go to Pochomil, go to Bar Jessenia. There you can get a lobster dinner for like $6.
If you're interested in zip lining, I think the best place to do that is at the Mombacho Volcano. It’s quite safe, costs about $11, and you can have a guide with you the entire time. I would also suggest visiting a small Nicaraguan town, such as Diriamo or Diria (I have family in Diria!). Diria has a lovely little church, Iglesia de San Pedro, in the central square. El Boquete is the name of an area of restaurant/bars that line the top of Laguna de Apoyo and you can easily get to el Boquete from Diria. The bars have a great view above the lagoon. Laguna de Apoyo is gorgeous lakeside as well. There are a couple of resorts around the lagoon, but Norome Villas is about the easiest to get to and they have a restaurant with great ceviche. And try or buy some Flor de Cana, it's a very smooth rum and there is a distillery in Chichigalpa. If you like coffee you should check out the Matagalpa region. Selva Negra is a coffee plantation with a lovely hotel.