The objective facts are these. Juniata ranks 97 in the Top 100 of America’s Best Colleges 2008”. It’s a small school (less than 2,000 enrollment) with a good student-faculty ratio in a rural setting. It has a religious affiliation with the Church of the Brethren.
SUNY-ESF ranks 85th, even better, in that same list. It specializes in your field and is fifth in specialized research colleges for productivity of its faculty. It is in an urban setting (Syracuse) and has a size similar to Juniata (1,544 enrollment). It has no religious affiliation.
One other fact. Tuition for out-of-state students is about half at SUNY ESF than at Juniata.
The decision of which is the right school for you is very personal. If it was me, I would be swayed by the chance to do cutting edge research in my field that SUNY offers. On the other hand, if you hate cities, it might not be right for you. Maybe learning in a religious environment is important to you.
You will be lucky to get to go to either place.