My favorites are probably:
01. The Human Equation
02. The Theory of Everything
03. 01011001
Buuut, I'd recommend you'd switch out 01011001 for The Source.
The Human Equation is 100% the first album you should listen to. It's nearly unanimously agreed to be the best Ayreon album, and it's not hard to see why. It has the perfect balance of interesting storytelling and characterization, good music, style shifts, nice individual songs, and good album flow. Fair warning, tho: Day 11: Love is the catchiest metal song in the history of the universe. It will be stuck in your head forever. Plus, it can be enjoyed without knowledge of the Ayreon story.
The Theory of Everything is probably the most album-focused of all the Ayreon albums. It's also quite a bit lighter than the rest (kinda funny, because it's sandwiched between the two much heavier 01011001 and The Source albums that preceded and followed it). It doesn't have much in the way of localized songs, but it probably flows the best out of all the albums. It's a bit lighter on the vocal side of things, but it makes up for that by basically being a "who's-who" of prog musicians (especially keyboardists...Rick Wakeman, Keith Emerson, and Jordan Rudess all on one album? Yes please) and having really strong characters and story. It can also be enjoyed without knowledge of the larger story, since it's separate.
01011001 is basically the exact opposite. If you ask me, it's probably the heaviest and darkest Ayreon album and it's the least "album-focused" and the most "song-focused". It has a lot of really strong vocalists, but the characters are fairly weak and the story can be a bit confusing to follow at times. That said, I'd say you should listen to The Source. It is the very first part of the greater Ayreon story, giving a lot of backstory to it. It's similar in tone to 01011001, but has a bit more of an album experience. Great vocalists still, and some really killer music.
If you want to follow up after tHE/ToE/tS, I'd recommend moving on to 01011001 next, then the first two albums, then Into the Electric Castle, and finally Universal Migrator (and maybe relisten to tHE between Electric Castle and Migrator...trust me on that one
). That's probably the most logical progression to try to follow the story.