We want to travel from Siena on a Sunday in July to Lucca by bus or train. From what I can see, this will mean going via Pisa. Will there be buses from Siena to Pisa and onwards to Lucca on a Sunday? We are thinking of spending a couple of nights in Lucca, before returning home via Pisa.

trains are usually the best thing to do in Italy

check out trenitalia

BUT i do believe that for Siena the train station is not close to the centre of town

Jen is spot on - take the train from Siena to Lucca. Most of the services go via
Firenze, where you will need to change trains. The total journey time is around
3.5 hours.
From Lucca to Pisa is also doable by train. The station in Pisa is San Rossere(about 5 minutes walk from the leaning tower)

For train times look at http://www.ferroviedellostato.it/ and select English from the link in the top right hand corner. You can put the station names in, and the day and time of your travel, and it will give you the trains.

You can also go to http://www.trenitalia.com/en/index.html

Both sites will take you to the same timetable and booking page

There is a bus from Siena to Pisa airport, you would then have to make the 5 minute journey by train from pisa airport to pisa centrale where you can get a train to Lucca (it is true that the station near the tower, San Rossore, is on the Lucca line, but the trains that stop there all originate from centrale which is closer to the airport). Here is the link to the bus service http://www.trainspa.it/sienapisa.html

However, the bus takes two hours then you need to get to centrale and pick up the Lucca train, so all in all it is probably easier to (and quicker) to take a bus or taxi to Siena train station (2 km from centre) and train all the way. You will have to change once, but I think it will be quicker overall. If you go to www.trenitalia.com you will see that you have two options. The fastest way is to change trains at Empoli it takes around 45 minutes longer if you change at Florence.

I hope that helps clarify your options.