Just wondering if it is possible to do this route in April or is it too dry then/is the weather OK?
Also, where are agents in Phnom Penh I can book this?
I've heard very mixed stories about safety/comfort as well - any recent update on this?
From everything online (blogs, wikitravel, and websites) the ferry as you know is best in the wet season, when the river is high (June to November, usually)
However, as the dry season approaches or ends, it's debateable. If the rain comes early, you could be ok. However April is quite well into the dry season, but still over a month before the rains - it'd be risky.
Not to worry though, they just have a work-around:
I've also read mixed opinions on the ferries - described on that site as "'local transport' and are of variable quality and comfort, often noisy, crowded and over-air conditioned. ". If you're an experienced traveller, you'll take this in your stride, while people new to the conditions might feel claustrophobic and unsettled, as well as overriding concern about the boats - they don't meet international standards of safety by any means, apparently (well, they do float...sometimes).
Your best bet is to get there and see how things are. The rain may have come early, and you'll be ok - in which case your hostel could surely direct you to an agent, or even book it for you. Alternatively they'll give you suggestions on what else to do - there are regular bus routes too, as that's the most popular way of getting between the two places.