Mathematically speaking, you should minimise the average number of additional dice needed to bear off all checkers. This implies a minimisation of the number of dropped rolls - rolls that do not remove a checker from your home, but only advance it further.
Suppose you move the three to the one and leave the six there on the first turn. On the second turn, you now need to roll a 6 and a {1,2,3,4,5} or a double {2,3,4,5,6} to clear both checkers with probability 15/36. Anything less will bear off one checker with probability 19/36 or nothing with probability 2/36.
On your third turn, you bear off the last checker with probability depending on the previous roll, but an average of 96.6% of the time, you're now finished. The remaining 3.4% require a fourth turn. If you had both checkers left, you bear off both 17/18 to finish and require a fourth turn for the remaining 1/18.
Overall, this is an average of 2.604 turns to bear off both.
A similar analysis finds that by moving the six to the four and leaving the three, you are 47% to finish on the second turn, and 50% to finish on the third turn. The average from this position is 2.553 turns to bear off both.
Note that in every subsequent turn, you are better positioned to finish on that exact turn by moving the six forward on first turn, not the three. The reason is simple: the single die roll has a uniform distribution and the pair dice roll has a triangular distribution. This means you are more likely to hit values in the middle of the range, either 3 or 4, and less likely to hit those at the ends, 1 or 6, while 2 and 5 fall in the middle. Since bearing off requires at least a particular number, and small rolls only bear off small numbers, it is more likely that a checker in the middle can bear off than a checker at the six. By moving checkers from the high end to the middle, you gain better chances of bearing off much quicker than by moving from middle to the low end.
You can test this yourself: set up a board with both colours in their own homes, white split between the one and six points, black between the three and four points. The vast majority of games will end with a black victory: white struggles to use middle rolls to move the high checkers forward, while black uses almost every turn to remove at least one checker. To really exemplify the point, use identical turns for both sides by rolling the dice once and playing them both with those numbers.
In terms of strategy, this means
Bear off the most checkers possible.
Move forward the highest remaining checkers that cannot be borne off.