My thought–speculating–is that Washington did not want retaliatory devestation of Boston. The Brits had already burned Charleston in the immediate Boston area, and some other coastal towns as well (one in New Hampshire, one in Virginia I believe–don’t have the names handy). They were bound to leave, we did not want them to leave a heap of ashes. Question for Peter, who has just finished McCullough–did Knox bring gunpowder as well as cannon? We had been seriously short of the former early in the Boston siege.
A few months later the issue came up again with regard to New York. Nathanael Green argued that, rather than trying to defend it, we should simply burn it. After the British captured it, following various battles in the New York area (Brooklyn, White Plains, Ft. Washington) a substantial fire did break out, and Washington was overheard to remark that perhaps some patriot had set it. It is possible that Nathan Hale’s mission was related to this. But there was no foreseeable possibility of retaking New York–we did not do so until late 1783–the calculus was different.
Alex Rose has just completed a book on spying and war-time New York–Alan Furst with flintlocks–so he would be up on any NYC-related details.