Yes 2003 64-bit was the first official 64-bit x86 windows and is probably the largest advance over 2000, and there really hasn't been anything since that is as large a technical capability addition.
I'm on the fence, but frequently say that 2000 was probably the best. Then I have to qualify that maybe the preview 64-bit XP or full win2003 might be first or in the running because 64-bit is such a major/critical feature to modern computer that if you wanted to sell a modern "Windows for business" release you would have to pick one of the 64-bit versions rather than rolling back to 2k.
I too ran 2k3 (64-bit of course on my athlon64) for a while as a desktop and technically it was fantastic, but eventually ended up switching back to XP with a few hacks to just avoid the general issue that a number of pieces of desktop software refused to run on a "server OS" without buying the server license for $$$$.
As to "the best OS Microsoft has ever made," it was OS/2 (which they abandoned in favor of the "hugely successful" Windows 3.0 which was clearly inferior on all technical accounts).
