NCAA spokeswoman Jennifer Royer e-mailed the following statement on Friday when asked whether her organization had any concerns about Thomas' arrangement.

"According to an official interpretation on June 6, 2001, NCAA member institutions are provided the discretion to establish their own policies regarding employment and income arrangements between their athletics department staff members and professional sports organizations. An NCAA coach must, however, still comply with NCAA bylaws as they relate to the recruitment of prospects and the scouting of opponents." 

http://rivals.yahoo.com/ncaa/basketball/blog/the_dagger/post/Isiah-Thomas-new-gig-could-create-a-conflict-of?urn=ncaab-260844&cp=3#comments

I take that to mean, that on the surface they have no problem with what the Knicks and IT are doing. But, if there is any sort of infraction, they will step in. If they step in, it would be aimed at IT and FIU. Not the Knicks, as technically the NCAA cant do anything to the Knicks. I also bet they would hit hard, to set a precedent and prevent this kind of thing happening again.

The NBA however is looking into it now (same link):

Amazingly enough, the NBA may end up being the organization that forces Thomas to choose between FIU and the Knicks. Since the hire could violate league rules that forbid college coaches from having jobs with NBA teams, spokesman Tim Frank told the Associated Press that the league is looking into it.

"We are reviewing the agreement, in consultation with the Knicks, for compliance with league rules," he said.

I am sure that Stern wants nothing to do with the Knicks causing a NCAA team to get sanctioned.