The verdict
If your customers already chat on WhatsApp and you are one or two people, start with the WhatsApp Business app. It costs you nothing to learn what people ask.
If support volume is growing and conversations need owners, history and a hand-over between colleagues, pick Intercom and connect WhatsApp to it. If you only want a simple answer, I would not choose Intercom just to read WhatsApp messages, and I would not run a growing team from a phone app.
My rule: choose the system first, then add the channels your customers prefer. If WhatsApp becomes your main channel, keep email or live chat as a fallback, because Meta sets the rules.