Any guess on noise magnitude and spectrum? Can't filter it?
6N136 is quite nice -- good and fast. Except that it has that pesky base lead, which picks up huge amounts of noise. (The datasheets will lie to you about this. The Fairchild datasheet, I believe, says it's good for quite a high CM dV/dt, but at the massive voltage step of 5V or something! Other ones have more realistic values, like < 1kV/us for a 100 or 1000V step.)
Fortunately there is help: the SFH6345 is identical, but the base pin is kept internal. It's just as fast, but now it's good to 10kV/us at 1kV step!
Any of the fancy ones, like 6N137 or HCPLxxx, with the amp/detection logic inside, are good as well, especially if you need the speed.
You might also consider magnetic isolators by then (e.g., ADUM2201). Beware that some of these are not guaranteed for DC operation (they communicate via pulses); the cheaper ones (e.g. Silicon Labs) don't make such a claim, and I wouldn't recommend they be used on DC-dependent codes (e.g., gate drivers). Digital data with error detection/correction should be fine.
My experience with ordinary things like 4N35 or CNY17 has been: as long as you're using it at a modestly low impedance (say 1k or less -- need not be in saturating mode), with suitable filtering, it's too slow to care about common mode noise. Two pin devices may be better or worse, since: although there's no base pin to pick up noise (a plus), you can't pull the dirty little secret of adding B-E resistance (47k or 100k being best IME) to speed it up, shunt noise and reduce CTR.
Tim