The 49ers took care of some big business on Wednesday as they locked up punter Andy Lee to a six year deal for a reported $20.5 million. Lee was going to be a free agent following the 2012 season, and while the team could have franchised their all-world punter, getting a deal done was likely in the best interests of both sides.
Moving forward, the most high profile player to consider for a contract extension is probably linebacker NaVorro Bowman. Guys like Ricky Jean-Francois, Isaac Sopoaga, Larry Grant, Dashon Goldson and Tramaine Brock are all expected to be free agents after the 2012 season, while Bowman is not a free agent until following the 2013 season.
The 2012 guys make plenty of contributions and there are reasons to get deals done, but given what Bowman did in 2012 and his current salary, a long term extension would seem to be in the cards. Football Outsiders took a look at 2011 defeats and ranked Bowman quite high. Defeats are defined by FO as any play (tackle, assist, pass defensed, interception, or forced fumble) that does one of three things:
1) causes a turnover
2) causes a loss of yardage
3) stops conversion on third or fourth down
Bowman ranked 11th among all players, and sixth among non-pass rushers with 27 defeats. If you go down the other breakdowns they've done, Aldon Smith had 21 defeats (thanks primarily to 14 sacks), while Carlos Rogers finished with 19 defeats.
The 49ers have done a great job securing the core of the team, with 23 of their 26 "core" players locked up through at least 2013. The key now is extending players beyond that to secure the long-term future. NaVorro Bowman is one such player, but he is in an interesting situation. After a quiet rookie season, Bowman blew up in year two. The 49ers know he is talented, but in negotiating any kind of long-term deal, the question is how you value his second year on its own in considering what he will do in the future. I don't think there's anything to indicate he won't be a long-term success, but negotiations have to be an interesting give and take given the single season body of work involved.