Brady is pretty much guaranteed to give you 250ish and 2 tds even with the injuries. Not great, but should be good for somewhere around 22-25 pts. He's been my keeper QB for probably like 8 years now and I really can't remember more than a few select games that he's given me less than 20.
Kap has more fantasy upside then Brady because of mobility and better targets, but the match up is brutal. Look what Sea did to Cam last week. I think Kap could just as easily get you 16pts as he could get you 30+. Look at the rest of your roster and compare how it matches up to your opponent. If things are looking pretty even, then I'd play it safe and go with Brady. If you've got a tough match up this week and think you will probably lose, then you may want to go with Kap and hope that he goes crazy again and helps you pull out a win.
Here's my dilemma for the week. Pick 3:
Cruz vs Den
Garcon @ GB
Torrey Smith vs Cle
Thompkins vs NYJ
Boldin @ Sea
An added element to complicate things is that I have Vernon Davis as my TE. If I play Boldin, that gives me 2 position players on the same team and if Seattle D balls out, then I'm getting hurt twice as bad.
Another added element is that I was able to pick up J Thomas on the waiver wire. So I have a decision to make at TE.
Last element is that my flex includes a TE option. So I could play 3 WR or I could play 2 WR and 2 TE. Decisions, decisions. Thoughts or suggestions?