Choose the right time and place
Unless everyone is making questions and the team was asked for opinions, you don’t want to challenge your boss in front of everyone. You’d better tackle your concerns one-to-one. Just don’t surprise-attack and don’t use emails: take an appointment and talk to them privately.
Extra hint: before you even start, make sure your issue is boss-worthy and cannot be solved among your peers instead.
Make it about the project, not about you
The key is not “I don’t agree”. It’s not your ego against your boss. It’s all done for the benefit of the project, the team, the company. All common ground between the two disagreeing parties. The key then is “I don’t believe this thing will work”.
Ask questions and focus on results
Assume you may be wrong and ask again about what concerns you. If the answer does not satisfy you, address your worries. Asking first will show that you’re not there to attack, but to understand and to improve.
When making your point, remember to highlight different outcomes. And don’t forget to use their language: speak of data if your boss is all about numbers, be emotional when dealing with a passion-driven manager… you get the point.
Respect the final decision
At the end, they’re boss and you are not. Theirs is the final decision and theirs the responsibility.
They may still know something you don’t - or they could just be plain wrong. As long as you’ve let your opinion be heard, you’ve done your best. Your boss will appreciate you for knowing your place - and if proven wrong once, they could learn to trust your judgment in the future.
All of the above works when your opinion is well advised, but also if your boss is more interested in results than in ego - and if your company culture allows for effective suggestions from employees.
If neither of these apply, it may be the right time to look for a better boss in a better place.