Area51 is in the list of SE sites of the new top-bar included.
But since I have 700 rep there it should be in my top 5 sites to be consistent.
BTW I don't get notified about new rep on Area51 as well.
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Area 51 is different and does not aggregate in the same way as all other code bases which makes it prohibitively expensive to load in the site switcher. The other totals we've gotten data aggregated to the point it's a single efficient query when not cached (also keep in mind it has to be re-fetched on the first hit after your reputation changes on any site).
We preload this section of the dropdown in the original page, so performance is absolutely critical here, it affects every logged in page load.
We aren't prepared to aggregate Area 51 at this time, or likely ever. It's a different code base that serves a different purpose (it's not Q&A) which would mean some schema changes to the network tables with contain homogeneously aggregated data.
So basically: if it were cheap we'd show it...but it's not and it's an very non-trivial amount of work to make it so (it has none of the aggregation system) or keep it current.