General pointers:

1. If you are booking far in advance, don't discount cheap direct flights. You should be able to use a popular flight finding site to find them.
2. AMS is a big well connected airport, by comparison Crete is far less connected (although it IS still more connected than many other places). So in terms of identifying options, this is a lesson to work backwards - look at who flies to Crete, and from where.

For using the miles you mention, you will need to connect (unless Krisflyer have a partner I am not aware of).

Avios:
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All the schemes that use Avios points (are they in a BA account? an Iberia account? or a .... account?) price per sector. But they do offer good short haul millage pricing. The question is just minimizing the taxes. (again compare this to the low cost direct flights). But if you are using Avios, I'd want to keep it to two sectors (i.e. single connection).

For Avios, your airlines that could make sense would be:
BA with connection in London (service from Crete is seasonal from LGW)
Air Berlin with connection in various places (all seasonal services)
Meridiana who are a new Avios using partner, not part of oneworld, and who do fly to Crete. Although I'm not singling them out - just mentioning in case not aware. Services again seasonal.

I got this from looking at the wikipedia page for Crete - work backwards if the destination is the smaller airport (i.e. the constraint).
The other starting points would be the crete airport website, or the oneworld.com timetable.


Generally I'd look at BA to BA connection booked from BA Exec Club account, or Air Berlin booked with Avios from a BA account.

Krisflyer:
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I don't know about the redemption rates of Krisflyer. But with star, look at who flies to crete (as mentioned above), that will tell you your options.

Although I don't know krisflyer redemption rates/value for money.