In this article it is said that "A BEC is a group of a few million atoms that merge to make a single matter-wave about a millimeter or so across." Does this mean that when they make a matter wave they are visible to the naked eye? Since a millimeter is big enough to see.
A Bose-Eistein condensate is typically a very, very dilute gas. While it's big enough to see in principle, in practice it doesn't scatter light strongly enough to be visible.
There are exceptions to this. Some BECs have been made that interact strongly with light. However I think that even in these cases they'd be invisible because the light levels used in these experiments are very low and too dim for the human eye to pick up.