going to give you a few suggestions,some easy reach from the main tourist areas and some where you may have to go on a bit of an adventure.
http://www.pivolod.cz/
this only opened up less than a year ago and I have made at least 6 visits, micro brewery on a ship, 6 good beers made in house, down stairs is a pub style area and does classic czech pub food, the main deck is more restaurant style and a more refined bistro/gastro pub menu.,I have eaten and drank in both places and the beer and food is excellent,service is also some of the best you will get in the city.In the summer the top deck (open air) does a grill menu , I have not tried this as it was not open when I visited in the summer (still being painted),it may be open in May depending on the weather.
http://www.u3r.cz/en/
another micro brewery (have you noticed the theme yet?)
on 2 levels , usually 4 or 5 beers available and they are very good, nice décor,great murals on the wall and some fun paintings .Food very good, again bistro/gastro pub style and service is pretty good.prices for the area more than acceptable.
https://www.pivovarnarodni.cz/
another micro-brewery (you will have got the theme now),only a couple of beers on tap and not my favourite ones in Prague ,good but there are better. Food is very nice again bistro/gastro pub style though I did find the portions to be on the smaller side.service is great and they have a nice outdoor area.
These are all in the main tourist area though Lod Pivovar is down by the river for obvious reasons.
This next place I am putting in as I have not made my mind up about it.
http://umedvidku.cz/restaurant/
This used to be my go to place in Prague but has changed dramatically over the last year or so,I had not been in the restaurant part for a while but went in with Czech friends just after New year, place was busy and service was diabolical (we gave then another 2 minutes to serve our food or we would have been out of there),seems to have sold their soul to the mass tourist market.
I was in their Oldgott brewery area the next day for a couple of beers as I do like it and service was a bit better but nothing great,will make another visit when I am next over to see if any improvement has been made.
Now for adventure.
http://www.podjuliskou.cz/en/
this is on the northern boundry of the city last stop on the 8 and 18 tram, great place and a Gambrinus themed pub, great food and in the summer they have a beer garden at the back doing food from the grill and it is superb.Great service too and beer is fantastic.Lost count of the number of times I have been in this place.
http://www.utopolu.cz/
one tram stop before Pod Juliskou, a real student dive pub with classic Czech food and surprisingly good Fish and Chips. good service and good beer,prices are unbelievably cheap.
http://www.kulatak.cz/
On Dejvicka roundabout and a minutes walk from the metro (trams are close by too), great food with huge portions, fantastic tanked beer and great service,prices are good too though on the higher end for the area.
https://www.pivnice-budvarka.cz/cs/budvarka-dejvice/
now this used to be my number one place in Prague , it might still be and I will tell you why. I have used this place on a regular basis for over 10 years, my local when in the city a fantastic old fashioned place doing great traditional Czech classics like your grannie would cook.Last July they closed it for refurbishment and tarted it up,completly changed the character of the place.The food menu is more limited and they no longer have my favourite Koleno (Pork Knee) but the food they are doing is still clasic Czech but like the pub tarted up but beautifully presented.Service was great over the New year period and I must admit I enjoyed my visits there ,beer was great but it is going to take me a while to get used to this new look.it is a short walk from Dejvicka metro and again trams stop nearby.
To be conitued,running out of Characters