How isolated do you need it? That is, what common mode impedance (at what frequencies) could you tolerate?
A comprehensive answer to this question, actually, would solve your problem at the same time -- where is the common mode noise getting in, in the first place? Answer: at whatever input connections have CM-diff conversion gain, or in-circuit nodes that are picking up ground loop voltage/current
Knowing a ballpark figure of those impedances and coupling factors, tells you exactly how much CM noise you can tolerate. Knowing the input CM voltage/current (what does it connect to? how much does it care/matter?) also tells you how much impedance you can tolerate.
If the impedance can be quite low, past some point (typically, this arises when the isolation is galvanic only), then use a "Y type" cap across the isolation barrier, to short out the noise source. Put a CMC in series with the DC-DC converter (one side or the other; 2-line chokes are much easier to find, so, that'd be the 5V side), and probably put a Y-cap between the converter's outputs directly. So you get a C-L-C filter, in the common mode, confining that noise to the converter itself. (A few extra bypasses and ferrite beads, on the local supplies, is usually warranted, too -- those things are usually nasty in both DM and CM. You've probably already tried this; consider this a note for completeness sake.)
If you need high isolation at most frequencies*, then you at least need to minimize capacitance, which will probably eliminate commodity isolator modules, at least the cheapest ones. Do consider the high voltage, low capacitance, reinforced or medical grade, types though -- they may offer value, even at the much higher part cost. Don't underestimate the total cost of a custom solution!
*All frequencies, simply isn't possible of course. There's always impedance somewhere, even if it's just self capacitance to free space (as would be the case for, say, a high-CMRR probe that's isolated with fiber optics).
If you do find you have to go with a custom solution, then consider CMCs again, this time as transformers. The coupling factor is poor (typically 0.98), but it's adequate for this power level. The capacitance and isolation voltage are great, and the price is phenomenal!
For a 5:+/-15V application, of course, the 1:1 ratio sucks. You'd have to consider, say, a 5:15V boost first, followed by a current-protected chopper/inverter, followed by a full wave doubler. All in all, it can be done in about a dozen transistors, or less with ICs, but probably not less than double the total PCB area of a commercial module/brick. Hey, you're bound to pay a price somewhere, just be ready to deal with it, whenever and however you do...
Tim