The choice really comes down to your ecosystem and how much you want to spend. If you're already deep in Apple's world with a Mac or iPhone, an iPad will feel more natural since your notes sync seamlessly and the apps work together better. But if you're not locked into Apple, don't dismiss Samsung - their tablets are genuinely good for reading and note-taking, often at a lower price point. The real differentiator isn't the brand so much as the screen size and refresh rate; you want at least 90Hz if you're writing a lot, since it makes the stylus feel way more responsive.
On the stylus question, I'd definitely recommend getting one that's designed specifically for the tablet rather than relying on whatever comes bundled. I borrowed a friend's tablet with a basic stylus thrown in and immediately regretted not upgrading - cheaper styluses lag behind your hand, feel plasticky, and make note-taking frustrating instead of enjoyable. If you're taking meeting notes regularly, that's actually something you'll use constantly, so spending extra on a decent stylus (or buying the official one for whichever tablet you pick) pays off pretty fast.
Budget-wise, you don't need a flagship model for your use case. A mid-range iPad or Galaxy Tab will handle PDFs and note-taking apps without breaking a sweat. Check if the stylus is sold separately first before you buy - some tablets bundle them, others don't - and factor that into your total cost. That'll probably matter more to your decision than the brand itself.