Yeah, that was Clancy's Debt of Honor. Good book.
Debt of Honor came out in 1994, the year following the first WTC bombing. I have no way of knowing how long Clancy worked on the novel, but at his prodigious pace (especially back then) I doubt he worked on it for much more than a year. Ramzi Yousef and Khalid Shaikh Mohammed went in to overdrive after the failure to bring down a tower in the '93 bombing and were well along in the Bojinka plot timeline by 1994. By 11 December 1994, Yousef made his trial run with the Phillippines Airline Flight 434 bombing.
It's doubtful (as some have suggested here) that the muzzies got their ideas from Clancy.