We have heard that travel to Greece, in particular Athens, is not recommended right now.

Absolute nonsense! Of course Greece, including Crete, is safe for two women traveling alone. Why wouldn't it be?

April is still off season, and ferries to other islands will be vey limited. Later in the month FlyingCat 4 should be sailing from Heraklion to Santorini, probably 3 days/week until the beginning of May.

Greece is a very safe country, you won't have any problems anywhere in Greece.
Athens is a 4 Million city, common sense is required.... but still it is a safe city.

Crete will be wonderful in April, if you go later in April there will be plenty of flowers everywhere, especially many endemic plants and flowers that can only be found in Crete.

Best way to see the island is with a rental car of course, that will give you full flexibility.
Using public transportation you only reach big cities, going to more remote places won't be very convenient. ( but still doable)

Arriving in Chania at 11 pm should not be any problem, just make sure to having secured your accommodation for the first night at least..

9 days is quite enough to see the highlights of the island.
You could split your time between Chania, Rethymno, and the east ( somewhere near Agios Nikolaos) and do day trips from there.

Not sure where you heard that travel to Greece is not recommended, 16 Million visitors had a different opinion in 2012... and the number will increase to 17. Million in 2013....

I wouldn't recommend visiting Santorini , you will end up spending most of your time in the boat... ( if you do the organized tour....which has a very early pick up and a return to your hotel at around 10 PM)

A day trip to Santorini from Crete is very expensive, and involves 2 hrs each way on a small catamaran, which can be uncomfortable in rough seas. Still, if that's what you want, here is last year's program, which will be updated for 2013 in the next month or so: http://www.ferries.gr/cruises/flying_cat_4.htm

As you can see, you get about 6 hrs on Santorini, then re-board FlyingCat 4 when it returns from Mykonos on the way back to Heraklion. FlyingCat 4 usually begins its season a week before Greek Easter, which will be on 5th May this year. As Easter is later than in 2012, I don't expect FlyingCat 4 to start running until the third or fourth weekend of April. I could be wrong though, so keep checking the above link for this year's timetable.

Thank you very much for the information. My daughter has just reminded me that the cheapest fares we found were both in and out of Heraklion. Is it better to fly into Chania and pay about 45 pounds more per person? It sounds like it will be better for us to rent a car. I am used to driving in California. What is driving like on Crete? We have crossed Santorini off our list. Are there other small islands near Crete that you would recommend? We are very excited to hear about the flowers perhaps starting to bloom Thank you again!

There is no other island close to Crete, Crete itself is a huge island..... the distance from West to East is 300 km.....

South of Paliohora in the prefecture of Chania there is the island of Gavdos, which is the most South point of Europe.
There is almost no infrastructure there.. apart from a small hotel..

There is also the island of Chrisi, south of Ierapetra, which is a beautiful small island with a great beach, there are organized tours that visit the island.

Flying to one city and out of another will save you from backtracking... the distance between Chania and Heraklion is 150 km....

Driving in Crete shouldn't be a problem.... some Cretans have their own driving style, but you won't have any problems at all

Thank you again. We have now booked our air into and out of Heraklion. It fit better into the budget. It appears that we can explore the east side when we arrive and then go to the west side (or vise versa) and then back to Heraklion to depart. Would Knossos be on your ideal itinerary? I've looked into your other suggestions and they all look great! Do you recommend reserving a car ahead or just getting a car when we need one? Are the street signs in English? Should I avoid driving in the cities? Thank you so much!

Knossos is a must see in my opinion, in combination with the Archaeological Museum of Heraklion.

I would recommend reserving a car ahead of time, since on the spot you will usually get higher prices.
I have mentioned this many times in other posts, but please chose one of the bigger car rentals instead of the unknown local ones for reasons of good and prompt service, since they have stations all over the island.

The cities in Crete aren't that big with the exception of Heraklion which has 150.000 inhabitants.
Driving in the cities shouldn't be a problem, and yes street signs are in both the Greek and latin alphabet...
Don't forget that Crete receives almost 2 Million foreign visitors every year, most signs will be bilingual

We are doing similar from Easter (May 5) for 14 days. Try Dimitris at www.autorentals-crete.gr for a reliable and best price deal I find.
Seems it will cost similar to get a taxi on arrival so you might as well pick up car at airport and you may decide to stay Ag.Nikolous or somewhere else outside Heraklion.....