I'm not sure which museum in Everett you're referring to. Up north in Everett there's the Boeing Factory with their associated corporate Future of Flight museum, which is fairly small. Factory tour is extremely cool though, I've done it at dozen times with visiting friends (pre-covid) and it was always neat.

And then south of Seattle at the Boeing Air Field is the Museum of Flight. I don't believe it's associated with Allen? Museum of Flight is alive and well, and I highly recommend anyone visiting Seattle swing by and spend a few hours there!