As a first time tech entrepreneur, I was confused if I should select one tool for mobile prototyping and other tools for implementation. I wanted to deliver my mobile app service as soon possible but I don't want to make mistakes when selecting tools. I have seen tools like Appcelerator, https://codiqa.com/ and PhoneGapp. Other than that should I also develop for android and iPhone separately, or should I use one of the above tools to develop once and deploy in different devices? Time and money is also a constraint for my startup. Please advice me. Thanks.
For really rapid prototypes than can be simulated on an actual device, Keynotopia is a great tool. The UI look can be identical to the platform OS. The interaction is tap-based, so you won't be able to truly simulate other gestures like swipes, pinch and zoom, etc (unfortunately).
With regards to your development question, cross-platform hybrid app development is very tempting (e.g., Phonegap), but I would not recommend it. My own startup went down this path and I deeply regret that decision. Sooner or later you will want the deeper integration and performance of a native app, which hybrid apps cannot achieve, despite their promises and protestations that they can. We eventually had to abandon our hybrid app and build a fully native one. Many others tell the same tale.