I can help! Lived and worked in Aberystwyth for 4 years. (Aberystwyth is 20 mins from Aberaeron, and has loads of B&Bs but also loads of noisy students.) Aberaeron itself - The Harbourmaster is the place to stay, is on the Visit Wales TV ad and is also (probably!) pricey. The food is superb too. There's also somewhere central called The Feathers, I think.
Don't know of any cottages in the region because I lived there. But there is a fab country house hotel in Rhydgaled (Chancery) - Conrah but it's closer to Aberystwyth than Aberaeron.
Is it a short break, or business or something? Do you need to be in the centre of Aberaeron or further out? (Just trying to find out why Aberaeron in particular! It is lovely.
This hotel is in Cilcennin which is very near Llanerchaeron (where the eisteddfod will be held). We passed it when we were house-hunting last year and it looked very nice! I agree with Essie3, the Harbourmasters is the place to stay in town - I'm tempted myself but only live 40ish minutes away so couldn't justify it really! There are several other small hotels/b&bs etc. along the harbourside so may be worth contacting the local tourist information for more options.
Gwesty Arosfa in Aberaeron itself was always very nice when dh and I used to stay there. Not been for, ooh 4 years, but it was always very clean and comfortable and great breakfasts of mackerel while looking out over the harbour.