I lived in KL for 14 years. Have visited Penang but never lived there.
KL has very good, but expensive schools. Alice Smith (Oldest in Malaysia, still a great rep and a true independant still Non profit. My eldest two DDs did A-levels there, since I left they have built an amazing 6th Form centre. Also Garden International (Taylors Group) or BRitish School (NordAnglia) are both good schools.
KL is as easy to live in as any big Asian city, English is widely spoken, most things available, driving is a nightmare, plenty of high quality accommodation with landlords of varying quality. Huge expat community. You could easily live in a bubble. Great hub for regional travel.
Penang does have schools as well. I have been back in the UK for 18 months now, when I left Prince of Wales School and St Christophers were the ones to look at, I have no personal experience, but a friend pulled her DS out of Prince of Wales, but that was a few years ago and I can't remember why (might have been the teachers were a bit ropey) Penang does have an expat community, but it's much smaller and has a more provincial feel. You would probably feel more in proper Malaysia there (if that's what you are looking for)
I did enjoy my time in KL, it was a good place to live, it has it's frustrations, but I kind of look back on them fondly now 