You can certainly send crash reports from different kinds of apps to the same Application in Raygun. The data will be processed and displayed perfectly fine, but there are some limitations that you may run into.
Most notably are the integrations. For example, the source-code integrations (that allow you to jump from a line in the stack trace to the relevant source code in your repository) can only be linked to a single repository. So this would not work well if your iOS and Android code are in different repositories. Notification integrations such as Slack can only be set up to send all notifications for that Application in Raygun to a single channel - which would be a limiting factor if you want to send them to different places or different team members.
Whether you send all that data to a single Application or split them out by code type is up to whatever work flow sits best for you and if the integrations I mentioned above would be a problem. Personally, I've found separate apps to be easiest to work with. If in doubt, you may want to try it both ways for some time before deciding on what works best. You may want to avoid releasing your app multiple times just to change API keys though, so you could start with manually sending some test crash reports from a test build, or try out different setups during a beta release or the like.
I hope that helps, please let us know if you have further questions about this.