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Boone is one of those guys that you have to just love. Blue collar type guy from Ohio State, he had great talent coming out of college, but Boone went undrafted in the 2009 NFL Draft, at least partially due to concerns about alcohol abuse. Once he put those issues aside, the 49ers recognized the talent he brought to the team not only at guard, but as the backup tackle spot. This caused the 49ers to offer a nice 6.5 million dollar contact to Boone in 2011 as a way to lock him up for a few years at an affordable price. Did the 49ers know he would work into a full time starter and help anchor right side of the line once Adam Snyder left town? The answer is probably not. Either way, Boone has been a bargain on an offensive line that features three first round picks.
Iupati has done everything and more to justify his draft status. Taken by the 49ers with the 17th pick in the 2010 draft, Iupati has helped Joe Staley make the left side of the 49ers offensive line one of the most steadfast parts of the team. Iupati is in the final year of his slotted rookie deal which has paid him 15.1 million dollars. Many would have thought that Iupati was a shoe in to get an extension from the 49ers when the time came in 2013, but that honor actually went to his fellow draft mate Anthony Davis who inked a 33.2 million dollar extension in 2013 that keeps him a 49er until 2019.
Ideally the 49ers would like to keep both Boone and Iupati past 2014, since they are home grown players that fit the team's identity to a "T". However, with top ten guard salaries average about seven million a year, the 49ers might be content to let Iupati walk and trade Boone this offseason (assuming he never reports) for 3rd or 4th round pick. The reason is they have Joe Looney, who the team feels can be a serviceable starter for them at right guard who also has a very cap friendly deal of only 1.2 million dollars over the next two years. A starting guard in the NFL for a shade under 600 grand in the NFL is a dang fine bargain.
Daniel Kilgore is another factor in this equation as well. Currently Kilgore is the 49ers' starting center, but can also play guard. Recently signed to an extension after Jonathan Goodwin left town, the starting center will be making a little around a million a year until 2017. With the drafting of Marcus Martin (4 years, 3 Million) in the third round of the 2014 draft, the 49ers more than likely see him as the future center (assuming he can stay healthy) and possibly moving Kilgore to either of the guard spots.
It appears, in this instance the answer to the question of which guard to pay is...neither.