What it boils down to is a) "how long is a piece of string" and b) "On time, on spec, on budget. Pick 2". This is another part of the art of electronics (and engineering in general) that isn't taught at Uni.
I'm afraid the only helpful tool is experience really. You need to know as much as possible about the project, clients have this habit of "knowing" in their head what they want and not telling you. Small things like "oh, did you not design the enclosure?" when you were clearly never contracted to do so, and it was never mentioned at any stage. I'm afraid timelines can be rather nominal at best. As a rule of thumb, double whatever seems about right. Only you can know how much effort is likely to be required and what resources you have.
If it is a small business and comparatively flexible, the chance of you hitting your date is higher than if you are in a 9-5 corporate entity, where work stops at 5pm. Of course the big corporates can bring in resources at any time, should the accountant see fit. But they rarely do, a late product just results in shouting and finger wagging. It seems obvious, but ask the client when they would like the product. Chances are that they have some date in mind which will help drive your milestones.
Oh yes, if the design is anything but simple, definitely build prototypes. Even the humblest embedded micro has silicon bugs which can be a show stopper. Not great if you have just ordered 10,000 PCBs. In a complex system, the prototype can go through quite a few evolutions between start and finish. There is nothing quite like having physical hardware in your hands to satisfy you and the client that the product exists and actually works.
Many management books have been written about Gantt charts and, so far as I can tell, they exist mainly to impress managers and marketers. Critical path / PERT charts are more useful, not because they make the dates any easier to hit, but because they can show up bottlenecks before they happen. They need quite a bit more detail than Gantt, but this detail allows you to make closer estimations.