No.
As the other answers mention, the ruling does not apply to the federal government, but rather only to the states. The equal representation of each state is defined by the Constitution itself and, therefore, it cannot possibly be unconstitutional.
However, it goes beyond that, even. The equal representation of each state in the Senate was a key compromise without which some of the original 13 colonies would not have agreed to ratify the Constitution (and, thus, join the current version of the U.S.) in the first place. The compromise was deemed so fundamental that a special provision of the Constitution was added in that specifically prevents this from being changed without the consent of every state.
no state, without its consent, shall be deprived of its equal suffrage in the Senate.
End of Article V of the U.S. Constitution
Any other provision of the U.S. Constitution can be changed through one of the processes described in Article V, wherein either 2/3 of each house of the Congress or a convention called by 2/3 of the states propose an amendment, which, upon ratification by 3/4 of the states, becomes part of the Constitution. However, changing the equal representation of each state in the Senate would require every state to consent, per the above stipulation at the end of Article V. And, obviously, that's not going to happen.
Simply put, even if Reynolds v. Sims had been intended to apply to the U.S. Senate, which it was not, it would have itself been unconstitutional and unenforceable (and any justice crazy enough to issue such a decision would probably have been impeached and replaced immediately.) The U.S. Constitution is very clear on the point that the Senate, not only can, but must be apportioned with equal representation from each state (and, specifically, that it must be 2 Senators from each state.) The Constitution describes this requirement quite simply:
The Senate of the United States shall be composed of two Senators from each state
Article I, Section 3 of the U.S. Constitution