The NFLPA updates their public salary cap report each day, and the latest update has the San Francisco 49ers holding $59,190,891 in cap space. They are a close second behind the Jacksonville Jaguars, who currently have $60,688,257 in cap space.
We know the 49ers have a ton of cap space, but it is worth noting the public salary cap report does not include every contract that has been signed thus far. After a player and team execute a contract, they then submit it to the NFLPA and the NFL Management Council. The latter is effectively the "management" side of the union/management relationship. Once the NFLPA gets the contract processed on their end, they update the public report.
For the 49ers, that means contracts for Ian Williams and Zane Beadles are not yet included. The 49ers have not announced either deal, which means they are likely still being processed on the 49ers side of things. That does not mean the deals will not happen, but they are just taking time for the formal execution for whatever reason.
The report does reflect the Phil Dawson and Thad Lewis contracts. I don't know what is included or not included in the Jaguars number, but according to Over The Cap, the 49ers are ahead of the Jaguars as well in cap space.
The 49ers cap space will decline once we get more specific numbers on Williams and Beadles, but they are probably going to have over $50 million in cap space even after those transactions. They could still re-sign Anquan Boldin, and they will likely add at least a couple more free agents to fill out the roster, but they are going to have a whole lot of cap space heading into the 2016 season, and likely to carry over into the 2017 offseason.