The Commander-in-Chief found, when he arrived, little to criticize and much to commend in what Putnam had done, for he had already stopped the Tories from furnishing supplies to the British fleet, had commenced to fortify Governor's Island and Red Hook, increased the efficiency of the works on Brooklyn Heights, barricaded the streets of New York with mahogany logs from the West Indies, and organized a "navy" of schooners and whale-boats, to cruise in the North and East rivers.
As Washington was absent much of the time in consultation with Congress at Philadelphia, Putnam was practically in supreme command; yet his arduous and important duties did not prevent him from attending a dinner on the first anniversary of the Battle of Bunker Hill.

In a letter written by an American officer describing this event, it is more than intimated that he was ever ready to accommodate when called upon for a song or a speech on such an occasion, for he says: "Our good General Putnam got sick and went to his quarters before dinner was over, and we missed him a marvel, as there is not a chap in the camp who can lead him in the 'Maggie Lauder's song.'" When in New York, Putnam's headquarters were on Bowling Green, where he later had with him members of his family, including his wife, who had also visited him at Cambridge, and had dispensed a generous hospitality at the Inman mansion; while Mrs.Washington (with whom both Putnam and his wife were in high favor) was at the Craigie house.

His son Israel was a member of his military family, which also included Major Humphreys (who afterward wrote his biography) and Major Aaron Burr, his military secretary.

His justifiable severity in proclaiming martial law, and in punishing Tories found guilty of harboring or assisting the enemy, incurred the ill-will of New York's inhabitants, and militated against his fortunes when later he fell into disrepute.
Plots against his life were formed, among them most conspicuous for its scheme of wholesale assassinations being that in which one of Washington's own guards was concerned, and for complicity in which this same man, Thomas Hickey, paid the penalty with his life, being executed on the 27th of June.

Two days later a large British fleet was reported off Sandy Hook, and by the 1st of July there were more than a hundred of the enemy's war-ships and transports in the bay.