Strangely enough, Peter appears later in the same issue in costume "applying" for a teaching job. He just jokingly says he wanted to see if Wolverine really did start a school.
Beast never had a specific reveal so I don't think he "knows". Reed does and the FF were the first to see Peter unmasked post-remasking. Tony has specifically said on numerous times that he doesn't know Spider-Man's ID post-unmasking. It's been implied Cap knows but he's never been present for an unmasking.
Those that have found out through Peter unmasking:
The Fantastic Four (Reed, Sue, Ben, Johnny)
New Avengers (Bendis had Spidey almost immediately re-unmask himself to the New Avengers, who at the time were Luke Cage, Jessica Jones, Iron Fist, Hawkeye, Mockingbird, Wolverine and Spider-Woman. Dr. Strange literally stmbled through the door seconds after the unmasking so he probably knows too. I found this quite odd and I think Bendis was really against the unmasking. He also included a throwaway line referencing the 616 unmasking the same month it happened in that month's Ultimate Spider-Man issue)
Captain America (never a specific unmasking scene but he clearly knows)
Miles Morales and a whole lot of other Ultimate Universe cast like Aunt May, Gwen Stacy, MJ, Iron Man, Nick Fury, and Captain America due to the events of Spider-Men.
There's probably a handful I'm forgetting but I don't think anyone else major has had an unmasking scene. In fact, I'm struggling really hard to remember if any villain has actually unmasked Peter so far and I don't think they have.
Those that always knew:
Those that deduced it:
(And now we get more into my opinion rather than concrete info contained within the stories):
Those that might've deduced it:
Harry Osborn- During "American Son" in Dark Reign, Peter's mask was practically hanging on by some threads. Their interaction after the story hasn't suggested anything but their interaction within the story really suggests Harry knew something was up.
The First Family and the Future Foundation- After Johnny Storm's death at the end of Hickman's Fantastic Four, Spidey joined the team full time. If he wasn't living within the Baxter Building, he spent a lot of time there. The First Family, besides Reed, Sue, and Johnny, included Valeria, Franklin, Nathaniel Richards, and Victor Von Doom. The Future Foundation consisted of several younger members of the MU who are generally considered intelligent. Since Spidey was on both teams, I think there's a safe assumption that people knew who he was. I'll also say that, while Hickman certainly seems fond of his world changing, mega plots, I thought he wrote an excellent Spider-Man and Peter Parker and would love to see him on a Spidey book some day.