An Aboleth is CR 10 and thus worth 5,900 xp. Deadly for 6 level 3 PCs is 2400 xp and and 6 level 4 PCs is 3000 xp. If the Aboleth is on its own, it is only worth half its XP when there are 6 PCs. So it is worth 2,950 XP. However, there are two points worth noting:
1. The CR 10 creature may have attacks that are so devastating for level 3 or 4 characters that they die instantly or cannot counter what it is doing. I don't have a MM with me at the moment, so I cannot say for sure.
2. The encounter building guidelines table is for 3-5 PCs. There are notes that everything should shift one multiplier up when using 1-2 PCs and one multiplier down when using 6-8 PCs. I didn't like that there were big jumps when going from 3 to 2 PCs or 5 to 6 PCs (i.e. for 5 PCs the Aboleth is 5,900 xp of difficulty but is only 2,950 xp of difficulty for 6 PCs). So I expanded the table by using 4 PCs as the standard, 1 PC for the low end and 7 PCs for the high end. I then filled in the rest of the table for all the numbers of PCs in between. In this circumstance, the Aboleth would still be worth 2/3 of its original XP or about 3,933 XP. Using that number, this would still be a deadly encounter for 6 level 4 PCs.
Given those two points, I would suggest either using a different creature or scaling the Aboleth back. The first question I would have for you is what level do you expect the PCs to be when they encounter the Aboleth? Second, how difficult do you want the encounter? At that point, you can use the encounter building guidelines to determine a CR for the Aboleth. If you scale back the Aboleth, I would suggest keeping the HP and scaling back on the damage to lower the CR. This will help keep the creature around for several rounds while limiting the risk of a quick PC death. This could fit in with the suggestions earlier in the thread of having the PCs strip away its abilities. If they are successful, they get the weaker aboleth. Otherwise, they get the CR 10 version
