netdata and prometheus are quite different. They can actually cooperate: netdata exposes all its metrics in a prometheus compatible format, so that prometheus can use netdata as a data collector.
In general, prometheus is a time-series database with an embedded scraper. For sources it cannot scrape itself it uses other data collectors (including netdata).
netdata is a real-time performance monitoring. The detail and amount of information netdata provides is probably too much for prometheus. Also netdata is distributed (you install it everywhere), while prometheus is centralized.
There is no good and bad in these things. Different things for different needs.
So, use the solution that suits you best...