Are they? I know they were eliminated from Redding...or whatever mining town it was they were in...but that doesn't mean they're extinct.
The eggs you see in Fallout 2 are the last generation of Wannamingoes to exist in the wasteland; the young Wannamingoes seen in F2 will perish in five years, and their parents a few years before that - an internal genetic clock will simply stop ticking, and they'll fall over dead. The Wannamingoes are a vicious mutant breed that had their moment in the sun, and now their sun has set.
To put the tombstone on their extinction, the largest known nest of Wannamingoes were wiped out when the Great Wannamingo mine was reclaimed by Redding with the help of a traveling tribal. The mother was killed, and the last remaining eggs were hunted down, stepped on, and then the remains were examined by local scientists and doctors who came to the extinction conclusions mentioned above.
Extinct.
Purpose
The idea, initially elaborated by community veteran Dan Wood, was to create a document that would serve as a total guide to Fallout: the history of the setting, the elements that compose it, the things that define it and the rules that guide it. It would also serve to tie off loose ends left by the games and to generally do some clearing up of things. It was certainly a good idea, especially as the prospect of someone who wasn't Black Isle making Fallout games grew ever more real. However, it really didn't work out that way.
Result
Instead of being a definitive, unambiguous guide to Fallout, Avellone's Fallout Bible became a sort of long question and answer session with fans emailing reams of queries to him and getting answers. Avellone would also usually toss in interesting bits of information about the games and original design documents, including the official Fallout timeline. Avellone made some mistakes here and there, many of which were corrected in later issues of the Bible thanks to fan feedback. The whole project was cut short when Avellone had to leave Black Isle.
Basically it was meant to set up what was canon.
And it was only later that it turned into a Q&A.
I've yet to see anything that contradicts this part of the bible so I will consider it canon until someone can come up with official facts for them not being extinct.