Hi, I have this webapp that allow users point theirs own domain to map to their profile.
So, this makes me wonder, if they decided to use their own domain, does it mean they need to configure their domain name's DNS to these?
ns1.digitalocean.com, ns2.digitalocean.com, ns3.digitalocean.com
Or do they point it to my VPS ip address?
Could you give us anymore details about the web app? It would help us give you better advice. Are you actually creating your own nameservers for its use?
One option that people use in similar situations is to create "vanity" namservers. This way your clients do not need to point their domains to another company's nameservers (in this case DigitalOcean). Check out this tutorial for more info. It should point you in the right direction:
How To Create Vanity or Branded Nameservers with DigitalOcean Cloud Servers
they would only need to add an A record in DNS to point to your VPS IP address.