It's not easy to say what my top five would be because it depends on what you expect of them. There are two kinds of Beatles books: books that make compelling reading, tell you things you didn't know, or entertain or fascinate you for one of several reasons, and books that are indispensable collections of data, a basis for further research or books you frequently return to for fact checking. There are some in the second category that manage to be entertaining as well, and some in the first category contain valuable information you might come back to at a later time. Lewisohn's Tune In is one of those rarer ones in the first category that are fascinating and entertaining, but also a source of precise data in the way of an encyclopedia, while his Recording Sessions is, first of all, a collection of information, dates and facts, but at the same time readable and enjoyable as a book you read from cover to cover.
I've read books of the first category that I enjoyed but take with a pinch of salt, most biographies for example. Many Years from Now is a great book exactly because Miles doesn't edit (correct) Paul's lengthy verbatim passages when Paul doesn't get his facts right. It's nice to see that it's not always those who lived through it who are correct.
Revolution in the Head is another book that straddles categories. Yes, Ian MacDonald is an opinionated author (and may even be hampered by specific likes and dislikes), but he was born just two or three years before the typical Beatle fans of the first generation, and that gives him a superb feeling for musical background and the cultural changes during that time. The long essay that opens his book is particular fascinating for fans from America and other countries because it paints a background of British culture and music that is essential for an understanding of the Beatles. In his analysis of songs he is not always right in who played what and is maybe too critical in his attitude. And yes, he doesn't particularly like George.
A very similar approach that focusses on the Beatles' Britishness but includes invaluable details about American culture at the time is Can't Buy Me Love by Jonathan Gould. Definitely makes my top five, exceedingly well written. Sophisticated and intelligent, if you can say that of a book, and quite a relief if you've just read three or four 'personal memoirs' of people who knew someone who once met John Lennon.
Here, There, and Everywhere is great in a way and annoying in another. There's a problem with journalists that 'help' eye witnesses and involved people to phrase their memories. In Emerick's case, some very vague memories take the form of word-by-word conversations. It is quite clear that the book was 'enlivened' and 'peppered' quite a bit and one should be aware of its limitations. And oh yes, he doesn't seem to like George either.
In terms of look-up books and sources I must mention John C. Winn's two-volume The Beatles' Legacy that collects all video and audio sources known today and dates and describes them. It's not without flaws, in my opinion, but is a great resource. Whenever I read something -- in a forum, for instance -- that I want to check, I use Winn and, of course, Lewisohn's Recording Sessions (and his Chronicle, if it's important, because it includes a few corrections of details mentioned in Sessions.
As for songs, a book I regularly check when I have consulted Ian MacDonald, is Tim Riley's Tell Me Why.
And, of course, there are many valuable internet sources. Not to mention all those books that I have not read!
(Kerouac, I hope this didn't overstretch your topic!)