There are many Monasteries as well as sites in Nepal. Most renowned ones are BOUDHA and SWAYAMBHU within Kathmandu Valley. Out of valley is LUMBINI (birth place of Buddha).
Here's a link - http://www.lumbini.org.uk/pilgrimage.html - hope it comes to your use.
There are so many Buddhist temples and sites across Nepal. If you are headed to Pokhara there is Pema Ts'al Monastery just outside of town. When I was there construction of a new temple was underway. You can visit during the day or stay for a few nights. Staying over night means you can eat and pray with the younger monks. They also offer Buddhism lessons. To see more information try here: http://www.pematsal-sakya.org
Also just a short walk down the road is the Tibetan settlement which has its own monastery and is very interesting.