Train from Schipol to Hotel in Leiden, Then to Dan Haag Museums?

are you aware that you don't really need tickets for those trips? Just tap in (credit or debit card or apple pay or android pay or your watch) and tap out and you will be charged the best fare. So for "A", tap in at Schiphol, tap out at Leiden do your thing, tap in at Leiden and out at the station you want in den Haag, tap in when leaving and tap out at Leiden.

Be aware that den Haag has several stations - the one nearest the central business district is den Haag Centraal, served by local trains, a dead end station. The through station used by both local and fast trains is den Haag HS. The HS is never spelled out but is for Hollands Spoor (The Hague Holland Rail).

Most of the others you may not use unless you are going to the beach.

If you buy an eticket, you’re allowed to interrupt your journey as long as it’s along the route the NS train planner advises. You can’t take a detour. Trains from Schiphol Airport to The Hague go via Leiden, which means that with a Schiphol-The Hague train ticket, you can get off at Leiden along the way.
Or you can forget about buying tickets and simply tap your debit/credit card whenever you enter and exit the train station.

Also; please mind the spelling of the name of the airport. It’s Schiphol with an H in it, not Schipol. Humans will know that you mean Schiphol, but travel planners might get confused and steer you in the wrong direction.

Trains in the Netherlands are like mass transit, with gates at nearly all stations to scan in and out.

You can use the NS Train app ( https://www.ns.nl/en ) to buy tickets, or just each of you use a credit card to scan in and out, which would be easiest. The trips you are making are short.

Since a train going to Den Haag will pass through Leiden, then it is not much extra effort to drop your bags at the hotel.

A couple notes specific to your trip...

At the airport, the train station is right in the main hall with escalators down to the tracks. There are no distinct gates, so you either need a ticket (paper or phone) or tap in at the poles surrounding the area.

Some of the trains on that route are Eurostar trains, for those you need a ticket and reservation, not worth it for you, so just ignore. There is also a class of trains called Eurocity Direct, you can get on those, but you must tap on the red poles on the platform to pay a supplement as well (or have a ticket, for that train, paper or phone) All other tickets, or by tapping in, are good for any other train on that route that day.

I might consider option C. Breathe Hotel is quite a hike from the train station. Fantastic hotel and neighbourhood though.

@Paul; if you take the train from Schiphol to The Hague, you won’t go via Rotterdam and you won’t take the highspeed train line. So your comments about the Eurostar and the Eurocity Direct are not relevant for the OP.

The Netherlands is basically a city state by world standards :-). It is about the size of a major US metropolis. The NS have been busy the last couple of decades transforming themselves in to a Urban Railway system, where the model is Japan. The aim is to have a train at least every 10 minutes at every station. So it is really just hop on and off at leisure.

Note that "tap on and tap off" works for all public transit in the Netherlands. But note also that, unlike in some other countries, you also have to tap off at the end. Don't ever forget that, or you will be charged the maximum fare...

Not all stations have gates. Where there are no gates look for yellow totems, with touch points. Schiphol is one of those stations without gates, and I see a lot of tourists missing the totems, and then they end up with an issue when they arrive at Amsterdam (or Leiden) where there are gates...

I just noticed your arrival date and the start date of the tour. You should know that Monday April 27 is our national holiday; Kingsday. I sincerely hope that your RS guide is familiar with this holiday and that they will make the necessary adjustments to the schedule for tour day 2 in Amsterdam.
Things may look relatively calm in the morning, but wait until after midday when the party gets in full swing and Amsterdam will turn into an absolute madhouse.. The streets and the canals will be full of partygoers dressed in orange and public transport within the city center is severely impacted.
I’m not saying you should avoid Amsterdam altogether, but “ take a break at a café along a peaceful canal” won’t be possible on Kingsday.
If you want to know more about what to expect of Kingsday in Amsterdam, see here; https://www.iamsterdam.com/en/whats-on/kings-day

I stored a pretty large suitcase at The Hague train station…was easy and there was good signage directing to the storage lockers. I’d do this option vs stopping in Leiden first; for me, the convenience and maximizing exploring time would take precedence over saving a few dollars. As others have mentioned, it’s super easy to just tap in and out on Dutch public transit so no need to worry about getting tickets in advance.

Thank you everyone for providing such great information. We'll do the tap on/tap off and go from Schiphol directly to Den Hague to make the most of our time there.

Regarding King's Day on Monday ... it will certainly make this a very memorable trip! Thank goodness our tour guide was born and raised in Amsterdam and has years of experience as a guide. It will be interesting to see if any part of the tour itinerary gets changed to avoid the biggest crowds. We're keeping a positive attitude to "roll with the changes" and just enjoy being there. 😎