Cribbage pone strategy for hands involving a run and a pair
I'm pretty sure the 'optimal' play is neither of the ones you mentioned!  Keeping 4,5,6,Q counts 7, gives you essentially equal opportunity for another 2 points off of any face card (you lose out on four extra points if one of the other two Qs comes, but that's only a 1 in 7 chance), still earns you all but two of the points you'd have had from 3,4,5,6 if you hit a double-run (though it slightly lessens the odds of it by cutting out the 3 as a double-run card), and gives your opponent just about the worst of the possible combinations for their crib (3Q).

To match Basicpract's analysis: you score two extra points off of any Ace (4), one point off of any trey (3), seven points off of a four or six (6), 9 points off of a five (3), one point off of a seven (4), two points off of a 9 (4) four points off of a Q (2), and two points off of any other face card (12).  This is 8 + 3 + 42 + 27 + 4 + 8 + 8 + 24 = 124 points off of the remaining 46 cards, for an average of more than two and a half points improvement and an average overall hand value of 9.7 points, compared to the 8 points from keeping 45QQ and the 9.61 points from keeping 3456 (but with a much worse crib to your opponent).