Hi Stellatus,
When do you plan to go there? My company helps people to travel & dive all around Indonesia.
All the Liveaboards who dives in Lembeh mostly not only do dive in Lembeh area but also the surrounding area such as Bunaken, Bunaken, Sangihe Talaud. If you only want to dive in Lembeh, you can actually stay in dive resorts.
Recently there are many new dive resorts there to suit every budget.
If you would like to go to Lembeh, I would suggest you to fly there from your country to Manado - the nearest International Airport that just located about 2 hours by car from Lembeh, to save spending money for domestic airline tickets. Because if you enter Indonesia through other big cities such as Jakarta or Denpasar, you will still need to fly to Manado - North Sulawesi from those cities.
Let me know by message, if you would like me to further assist you.
Cheers,