Well I think there could be, and maybe were several interlocking reasons for Ruby's demise.

First of all he was a very independent hood. He had a lot of money out, and most of it was his own, on his own. And although he needed "backup" from the mob for protection against guys taking shots at him, he wasn't in love with wise guys. So by befriending these Irish kids in his mind at least, Ruby felt he had some independent muscle. Supposedly he even utilized this Jimmy Coonan as a driver/bodyguard of sorts on occasion. If thats true then it shows how Ruby thought he was in control of them as his little army so to speak.

The Westies on the other hand were really a bunch of broken down valises who welcomed the opportunity to borrow money from Stein under the guise of shylock money. And although they may have only received $30,000 to $40,000, or some such figure from Stein to work with (a tidy some in 1976-77) it was not a fortune to Stein. But to these idiots it was.

At some point they figured it was cheaper to clip him than pay him.
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As far as the Javits Center goes, its in the heart of Westie country (the mid-westside - Hell's Kitchen), and they usually controlled that little area for the most part because there was nothing really there. But when construction on the Javits Center started, the mob wanted it.

Mickey Spillane, their Irish leader based from Woodside in Queens was supposedly killed by the Genovese because he tried to hold his own against them.

But as far as Ruby Stein getting killed over Javits, or actually having any direct connection to those events I'd look at that dubiously. By and large I think Ruby was just trying to work the "middle ground" between the Irish and the Italian mob. Trying to tip toe through the tulips, and he paid with his life.

As I stated earlier, IMO he should have just stayed away from them altogether. They were mostly loose cannons. Drunks, druggies, screwballs, and wild men who had little regard for anyone. They didn't even really understand the protocol of the underworld. They were really just a glorified street gang.

Even the old Irish based Arsenal Mob led by Eddie McGrath and his brother in law Connie Noonan in the 1930s-1960s were better plugged-in than these Johnny come lately's.