Alfie Burns, the black sheep, An seo, Against the grain, 57 the headline, L.Mulligan grocer are all great pubs. Black bird is another. There really is a great craft scene going on in Dublin now so a great time to visit. AFAIK Guinness is the only brewery in town running tours. Most of the breweries in the city are pretty small operations so don'y run tours etc.
I'm sure I'm missing some names if they come to me I'll update!
PS. If you want to go get just a great pint of Guinness but not have any craft beer I'd suggest The gravediggers pub or The long hall. The best pints in town IMO.