The Northwest Ordinance of 1787 said that the territory northwest of the Ohio River should ultimately become at least three, but not more than five, states. (It ultimately became five states plus part of a sixth. I happen to be sitting now in that part of that sixth state.) But they did not at that time propose any particular new states.
In 1784 Governor George Clinton of New York asked Congress to overthrow the government of Vermont, which he considered a district in rebellion against New York. A committee in Congress recommended instead offering the rebel regime admission to the Union as a new state. Neither that proposal nor Clinton's passed. Although the committee recommended that Congress make the first move rather than waiting for a petition from Vermont, this is not fully a case of Congress making the first move, since they had been approached by Vermont on previous occasions. Vermont had been turned down because of objections from New York, which claimed Vermont.
Both of the above events involved the Congress of the Confederation rather than the later two-house Congress consisting of a Senate and a House of Representatives.
In early 1791, Congress acted first to admit Kentucky, but that state was not to be admitted until well over a year later, and then to admit Vermont with only two weeks' notice. After negotiations between Vermont and New York, Vermont had submitted a petition, carried by the two lawyers Nathaniel Chipman and Lewis Morris to President Washington.
The legislature of Virginia had consented to its western district becoming the state of Kentucky. I don't know whether the proposal was submitted to Congress by the Commonwealth of Virginia or by statesmen of the proposed new state, but I doubt very much that Congress proposed the new state. I think the Virginians saw advantages in greater southern representation in the Senate and maybe also wanted to be free of expenses incurred in governing so large a region. Certainly at least one New Yorker, Alexander Hamilton, wanted Vermont admitted in order to get greater northern representation in the Senate, but it was the state of Vermont that submitted the petition.
Has Congress ever initiated the process without first receiving a petition?