I live in Prague, it's amazing for vegans! Will you be in a group of people with mixed omni/vegan diets, or are all-veg places ok?
My favourite place is Moment Cafe. It has good breakfast options (pancakes, omelettes, waffles), lunch and dinner options (the bagel with seitan and cheese is spectacular, but there's also a daily menu to consider) and an amazing cake counter. It's all vegan, and really nice.
I also like Plevel, which has two locations, one right by Wenceslas Square. It always has some traditional Czech/Eastern European dishes on the menu, and it's probably your best chance to try them.
Puro is nice, and it has a little Veganz shop inside. It's a small place, but it has nice fresh food. They have a changing weekly menu and aren't open in the evenings, so it's good for a lunch. In summer they also have an ice cream stand outside.
Radost FX isn't all veggie (it serves fish too), but it has a good menu. I've never been in the evening, but they have quite a few vegan options. The weekend brunch is nice, especially the vegan tacos.
Maitrea and Lehka Hlava are quite fancy sister restaurants in the city centre and people usually rave about them, but I don't think they're really worth your time, unless you're short of other options. Etnosvet is also fancy, but not great for vegans (the lunch buffet is quite good though, and there is a little vegan bistro next door - I've only ever had a cake from there, but I hear it's good).
There are loads of vegan buffet places, including a number of Loving Huts and Dhaba Beas (Indian, not all vegan but everything is clearly labelled).
Also, there are millions of raw places, but I don't know that much about them I'm afraid.
I have a lot of reviews on my blog, if you have the time or inclination to browse the Prague section here: https://herbivoresheaven.com/travel-in-europe/
Let me know if you need places for an omni group, or if you're not staying in the city centre, I might have some more advice!