Mr Trump looked set to take nearly all the 95 Republican delegates at stake.
He said his nearest rival Ted Cruz was "just about mathematically eliminated".
With more than 98% of the results in, Mr Trump is leading with just over 60% of the vote while Mrs Clinton has just under 58%.
US networks projected that Mr Trump had won in his home state barely seconds after the polls closed at 21:00 EDT (01:00 GMT).
Speaking at Trump Tower in Manhattan, he said: "I have to say to the people that know me the best - the people of New York - when they give us this kind of a vote it`s just incredible."
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