I'd take 2000, because the amount of 2003 servers out there compared to 2000 is low. The majority of companies out there with big servers have either migrated to 2000, or are clinging to NT4, and will be going to 2003 sometime in the future.
Plus, 2003's features are more similar to 2000 than 2000's to NT4, so you'll find the 2003 course easier if you take 2000 first.
Just my 2p's worth
Dopefiend