The atmosphere each set of supporters can generate is cyclical and changes over time. Usually, fans create a brilliant atmosphere when they overperform (or underperform).
Here are some examples:
1. Newcastle are having their best period in the last two decades. Fans are brilliant and loud right now. When they got relegated, their gates were much lower, and the atmosphere was very poor.
2. Arsenal fans have improved in the last two/three years. No coincidence that they're back in the Champions League and challenging for the league title. For the previous decade, they were amongst the worst in the country for noise.
3. Stoke was heralded as one of the toughest away games in the country and their fans dubbed the noisiest when they had just come into the Premier League. Now they're an average championship club they barely fill half the stadium.
4. Leeds fans were mostly brilliant in the PL, but a couple of years earlier they were getting tiny gates for most games.
5. Does anyone remember Bolton under Big Sam? They got that place rocking often. Now, again, they struggle to fill half of the stadium, and it's silent.
6. Everton have been terrible the last few seasons, but their support in last season's 'run in' was pretty special. Other than the odd game there when they can raise the atmosphere, their support (especially away from home) is really, really quiet.
There are tons of examples, and each club will have their own periods where they've had brilliant atmospheres and shit atmospheres. The key influence on this is over/underachieving compared to their own club's recent history.
For us, our 'standard' season is winning the Premier League now. It's really hard to overperform for us. If we had a shit season, our atmosphere would probably be defiant and brilliant... better than what it would be if we cruised to another Premier League trophy.
There are things clubs can do to alter the atmosphere slightly (logistics, pricing, infrastructure, engagement), but on the whole, they'll have a much lesser effect than what's happening on the pitch.