My internet link comes from a modem configured by the provider, which connects to my Mikrotik on eth1, while my LAN connects on eth4.

When configuring a DHCPv6 Client on eth1, I can obtain the IPv6 address but not the prefix.

In this case, would the best option be to configure a DHCPv6 Relay? I've tested this, and LAN clients can obtain the IPv6, but they can't even ping the Mikrotik for some reason I don't figure out.

Or would it be better to configure a DHCPv6 Server? In this case, what configuration should I use?

Better ask your ISP about possibilities. Either they could configure their router to hand out prefixes (preferrably larger than /64, /60 would be fine), or to bridge mode do that your MT would be talking to tgeir core directly (I guess tgat in this case your MT would receive prefixes).

The way it is now, MT's WAN side is part of ISP's LAN. But MT's LAN side is not. And when LAN client tries to communicate with your router, router sends reply via its WAN port (because that's where it thinks the /64 subnet is).

There's another possibility (don't know if it's feasible for you): keep using ISP device as router and reconfigure MT into switch (and AP).