It’s apples and oranges.
WaniKani’s main focus is on comprehension, using a very rigid system of radicals -> kanji -> vocabulary. WaniKani’s main advantage in my opinion is that everything is automatic. You don’t need to worry about creating a study plan, don’t really need to think about the question of “What should I study next?” or “How should I study?” you don’t even need to really worry about how much you want to study at any given time, since WK does all of that for you. And WK provides tools to aid you in remember every single kanji and most of the vocabulary to boot.
Heisig’s main focus is on writing the kanji, and understanding the meanings. It doesn’t even include readings of the kanji, or sample vocabulary as far as I know. It also doesn’t even have mnemonics for remembering all of the kanji, expecting you to create your own after a certain point. However, there are lots of resources that you can find online for readings, mnemonics and so on, if you really like. I personally think that’s a little bit of a hassle.
Another system is Kodansha’s Kanji Learner’s course. It turns the WaniKani system on its head, teaching radicals and vocabulary alongside kanji, so you learn everything at once. It also provides mnemonics, which are arguably more ‘professional’ than WK’s (no pop culture references, fewer ‘silly’ radical names, etc.). But again, you need to handle study and review on your own, usually by downloading pre-made Anki decks, but there isn’t much support beyond that.
I would say WK is the easiest system to use, since you don’t really have to think about it much. If you enjoy WK’s style (for mnemonics for example), and don’t mind that the pace is rigidly controlled for you, I would say it’s the best system. Heisig is best if you want to focus on writing kanji, and understanding the meanings only, focusing on vocabulary and everything else at another time. Kodansha would be best if you want to control your own pace of study, or if you find the WK mnemonics a little silly for your taste. However, mnemonics are only provided for kanji, not vocabulary, which might be a factor for you as well.
Either way, I would not say any particular system is “best.” It all comes down to your personal preference.