I actually made an "in order" list for my friend when she started reading them, so I happen to have that on hand...
Order:
1, 2, 3, 4, 5, 6, 7, Megamorphs #1,
8, 9, 10, 11, 12, 13, Andalite Chronicles,
14, 15, 16, 17, 18, Megamorphs #2,
19, 20, 21, 22, Hork-Bajir Chronicles,
23, 24, 25, 26, 27, 28, 29, Megamorphs #3
30, 31, 32, 33, 34, 35, Visser,
36, 37, 38, 39, 40, 41, Megamorphs #4,
42, 43, 44, 45, 46, 47, Ellimist Chronicles,
48, 49, 50, 51, 52, 53, 54
If you're going to be reading the Alternamorphs, I'd say the first one should be read after book 11, and the second should be read after the David saga (books 20-22). But this is if you're reading them at all. They really aren't worth it.