The "best" perks can vary based on play style. Some of the chem perks can be considered the "best" perks for one character simply because of how powerful chems can make them with no downsides because of said perks. I'd say the only perks that are undeniably the best are the perks that just increase damage with your weapons. Rifleman, Gunslinger, that sort of thing. Those also vary depending on the kind of weapon your character uses. Me personally, the likes of Better Criticals, Critical Banker, Grim Reaper's Sprint, Four Leaf Clover, Gun Fu, and any perk that contributes to more sneak damage is the best for my character.
With that said, I find it easier to name the worst perks because for a good amount of them, they're just flat out useless for any character. Anyway, in no particular order:
1. Awareness. A convenience at best, a pointless convenience at worst.
Basically sums it up:
Spoiler Getting info on damage resistance is useful to some degree, but with human enemies you can easily determine that already based off of what they're wearing. Leather armor means energy resistant, metal means ballistic and so forth. One should already know this info if they have ever worn armor. The perk is already unnecessary for half the enemies in the game. As for every other enemy, well, just use common sense. Radiation damage is obviously not effective towards everything that isn't human, poison to radscorpions, robots are weaker to energy, etc. But even then, these are resistances that are very specific to only certain enemies. Most take damage from ballistic as much as they do with energy regardless. And honestly, in how many combat situations do we actually consider how resistant an enemy is to a specific damage type anyway, and how much of a difference did that consideration make? We're just going to shoot them regardless with whatever weapon has the highest damage and it won't matter how resistant they were. So why bother knowing the specific numbers behind it?
When it comes to allowing you to see what level an enemy is, the game already tells you when an enemy is a significantly higher level when there is a skull next to their name. Besides that, you should be able to tell how dangerous an enemy is just by looking at them. If it's a mole rat, kick it aside. If it's a Deathclaw, be wary. Simple as that. Only use I see in seeing their level is knowing what you can intimidate with the Intimidation perk.
So in my opinion, the perk is far from essential, but not necessarily a good enough convenience to have either.
2. Lead Belly. Why are you eating junk food and drinking water?
3. Almost every Endurance perk. I admit, my personal bias against Endurance is showing here, but the over abundance of stimpaks and radaway found throughout the game world (of every Fallout game) negate a majority of these perks and the attribute itself. Leveling up gives you all of the health you need.
4. V.A.N.S. If you actually need this perk, you have much bigger issues to be concerned about than getting lost in the game.
5. Medic. The over abundance of stimpaks and radaway found throughout the game can negate this. Although this could be of use in Survival. Curious about how effective it is on that difficulty.
6. Scrapper. You shouldn't have too much issues getting the materials you need in the first place so long as you're marking them. Plus, its more weight to lug around if you're picking up every weapon and armor to scrap at a chance of not getting the material you're looking for in the first place.
7. Nerd Rage! Despite fun, you shouldn't be aiming to get your health so low in the first place. Seems far more efficient to just use Jet and go for the chem perks and it comes without the risk with such low health.
8. Fortune Finder. It's never hard to make caps in Fallout.