hi jessica
first i thought of allergies, but since you said the baby takes the milk better by bottle, i don't think it is that.
i think there is something different about the mechanics of baby taking the milk by breast, and baby taking the milk by bottle.
these could be factors: flow, overactive MER, oversupply issues. you already explored this somewhat and you feel this is not it.
the next thing would be respiratory issues. the baby may be able to stop and breathe easier on the bottle because there is no hard/fast letdown,
the baby can stop to mouth breathe without losing the latch. also positioning can be an issue and this often correlates with respiratory issues,
as baby may have his head flexed or otherwise feel or be obstructed during bf. so very closely observe the feeding if you can to look for 
clues. in the meantime, have mother express frequently and bottle feed if that is working, if she can comfort nurse or nurse on a less full breast
to keep the bf relationship going. perhaps a swallow study or speech pathologist assessment/


Laurie Wheeler, IBCLC, MN, RN
Mississippi, s.e. USA

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