Perhaps you are right, but I rank the Louisiana Purchase, the Lewis and Clarke Expedition (which I am almost certain he commissioned but not absolutely certain as I am writing this), and the abolition of slave trade as extremely significant.
The Louisiana Purchase was a bold act that he (as a strict constructionist) arguably had no right to do. However, it set the table for manifest destiny that dominated 19th century politics and served as the backdrop of many major accomplishments of future administrations.
The Lewis and Clarke commission was a minor thing for someone to commission (not minor to the Lewis and Clarke crew to endure and accomplish, mind you). Whether he had the forethought to realize it's import for the 19th century might be argued, but is is inarguable that it was an extremely significant accomplishment for the future of this nation. Perhaps it compares very favorably to the race to the moon. The accomplishment itself is amazing, of course, but its execution was not the most significant thing. All the things discovered, invented, enhanced, etc., in putting a man on the moon and the propulsion of these things via the private economy to escort us into and beyond the information age is the enduring legacy of the race to the moon. Likewise, most every significant accomplishment of the 19th century traces its roots and owes tribute to the Lewis and Clarke expedition and the Louisiana Purchase.
The abolition of the slave trade was an important act that set him apart from virtually every other 19th century President until Lincoln. Virtually all of them "kicked the can down the road" on this issue until Lincoln. None that I remember even lifted a finger to use the bully pulpit to even try to move public opinion. And according to some Lincoln would like to have done the same but to his everlasting credit (pure motives or not) he did embrace it and abolished the practice of slavery via the civil war.
Again, I am not a scholar and someone more knowledgeable than me may correct me about the slavery issue (it could be that other Presidents indeed did try to do something to help the slaves) or the Lewis and Clarke Expedition commission date, but if I am right I think these accomplishments significantly shaped the 19th century adn beyond for this nation.
While in no way diminishing the astonishing accomplishments of the Lewis/Clark expedition, the plain fact of the matter was that the Louisiana territory would have been explored sooner or later, probably sooner, in any event. There was no perceptible shortage of pioneers, adventurers, opportunists, and/or traders in the U.S. in 1803. Jefferson deserves the credit (with not a little prompting from several Western politicians, btw) for commissioning the exploration, but can hardly have expected the cornucopia of discovery that unfolded. Again, a bit of good luck -- not despising luck, mind you, but let's not confuse lucky results with ''greatness'', however defined. By applying that sort of standard, one might have to conclude that the odious Bent Willy was ''great'' because he was bloody lucky enough to infest the office just as the major effects of the Reagan tax cuts were being felt throughout the economy.
The president who never gets enough credit IMNNHO (besides Coolidge, of course), is Madison. Jefferson left him a domestic economy in near-shambles, a Federal budget in almost complete disarray (read Nevin, among many others, for a description of this ugly situation), and with a trade war (essentially) with Britain. By the end of his term, Madison had resolved the trade war VERY favourably, somehow had managed to win that silly war that resulted from the trade war (hardly a mean feat, Britain being what she was at the time), had quelled the New England separatists, had initiated much more advantageous funding procedures (the banks' loan-origination fees in that day were stunningly outrageous, and Madison, while not completely able to stop their practices, curbed them rather sharply by introducing them, quite involuntarily, to the concept of competition), and -- by dint of NOT intefering much -- had seen to getting the economy back onto something resembling an even keel. Significant accomplishments indeed for the president of a 20ish-year-old nation with no international standing, nor any international credit before his advent.
However, Madison did, inadvertently I presume, stick America with that insufferable mediocrity Monroe -- so perhaps he shouldn't move TOO far up the list (g!).