Famously, it's known that the water of Minetta Brook can be seen from the surface at a marble fountain in the inner lobby of #2 Fifth Avenue (which is just on the north side of the park-- where Fifth Avenue hits Washington Square North).
However, it seems likely that the fountain is no longer supplied by the historic stream, if it ever was. A 1930 NY Times article told about the exposure of the brook in this fountain, but I suspect whatever supplied it has been replaced by standard NYC water supply water (if it ever was Minetta water, and not just a publicity stunt.)
According to the Native's Guide to New York by Richard Laermer (W. W. Norton & Company, 2002), for example, Minetta Brook "dried up in the mid-1800s" and the 2 Fifth Ave fountain merely "symbolizes" Minetta Brook. (Although the plaque on the fountain says that "A brook winds its erratic way beneath this site," and explains that over time Minetta Brook-- sometimes referred to by its nickname 'Devil's Water'-- "has settled underground.")
Despite the improbability, other walking tours and guidebooks still suggest that the fountain is truly Minetta Brook water. Does anyone know any more about this? Please email me if you know! Also if you have a snapshot of the fountain, I'd love to add that to this post-- email me at firstname.lastname@example.org. Thanks!
I've also been told the stream is visible in a fountain at at 33 Washington Square West, which is at the western edge of the park.
Native's Guide to New York: Advice With Attitude for People Who Live Here--And Visitors We Like
By Richard Laermer
Published by W. W. Norton & Company, 2002