> I have moved some of them onto a simple VPS with DO for now but would like a better long term solution (i.e something managed).

> The main problem I am having at this point is that given they are NGOs money is a big issue and finding something that would work with their price range and isn't at the Godaddy level is proving to be a bit of a challenge.

These statements contradict each other. If money is an issue, you're going to have a hard time finding someone to manage an environment that small.

S3 + Jekyll are out if you need SSL. Have you thought about Docker containers on Digital Ocean with Cloudflare in front of the site (free tier comes with SNI SSL)?