If staying in town you can easily do it yourself with a full-day taxi. Patan Durbar Square is good - have a tea in the garden restaurant. Also the small town of Kirtipur (10 minutes from town). Lunch or dinner or Caroline's at Babar Mahal. And a look at Bodha also worth it. That gives you a nice overall perspective of the city.

If you want a guided city tour - or a half or full day trek or similar (easy to do depending on weather) you can check with socialtours.com. Highly rated and offers more than cookie-cutter options.