Both Are Valid
Nigerian universities accept both WAEC and NECO O-level results, provided you have the required credits. Many students write both: WAEC in school and NECO as a backup or as a private candidate.
Differences Students Notice
The styles of questions are broadly similar, but candidates often report that NECO papers contain more recall-based questions while WAEC leans on application. Timetables also differ, so you can prepare for both with a single set of notes.
Practical Advice
Whichever you write, aim for at least five credits including English and Mathematics in a single sitting. Check what your target school will accept before you decide to combine results from two sittings.