When will you travel?
How is your full itinerary?
Puratto Kodama is not a ticket but a tour package, which is offered not by JR Central [JR Tokai] but by its subsidiary company JR Tokai Tours.
Please note that Shinkansen trains run not via Osaka Station; you disembark at Shin-Osaka Station.
I am going to Japan (Tokyo) for the first time with my wife and 3 y/o daughter. I will be staying near Itabashihoncho Station Then, Shinagawa Station seems more easily accessible than Tokyo Station.
Shinagawa Station sounds better also because it is much simpler and there is only one Shinkansen zone; Tokyo Station is shared by two JR regional companies who have Shinkansen zones separately, which means you should choose a correct Shinkansen gate.
One possible demerit of your embarking at Shinagawa is that when you don't reserve seats, you might not have seats which you like best, because Shinagawa is the second station (after Tokyo Station) for almost all the westbound Shinkansen trains connecting Tokyo and western Japan.
(One exception is Nozomi 99 bound for Hakata, which starts from Shinagawa at 6:00.)
On the condition that your 3-year-old daughter (accompanied by her parent) does not solely use a reserved seat, she can travel by Shinkansen free of fees.
In that case, I recommend that you and your wife reserve Shinkansen Nozomi or Hikari train seats and have a ride with your daughter on the lap.
I'll be going to Osaka on Sunday, how is station during Sunday? On Sundays there is no morning commuters' rush; when you head to Shinagawa or Tokyo Station in the early morning (while most local travelers have not started their trips), I suppose you will not get packed in a JR Yamanote Line train.
[From Itabashihoncho Sta. to Shin-Osaka Sta.]
Itabashihoncho Station (I-19) is on Toei Subway Mita Line.
You can take a train for about 8 minutes until (I-15) Sugamo Station.
Sugamo Stations of Toei Subway and JR are equipped with escalators and elevators.
You can make a simple transfer to JR, via a concourse outside Toei and JR gates.
You take a JR Yamanote Line train (on the outer or inner loop, which does not make a big difference in the required time,) from Sugamo Station for about 35 minutes until Shinagawa Station.
In Shinagawa Station, you pass through Shinkansen North or South Transfer Gate to the Shinkansen zone.
http://english.jr-central.co.jp/info/station/_img/shinagawa_L.jpgYou confirm (on the electric signboard) the track number for your Shinkansen train, then go up to the platform.
When you have reserved seats, you check the car number on your Shinkansen tickets and find the position for that car.
When you don't reserve seats, you go to the position for a car of Non-Reserved seats.
Shinkansen trains which go beyond Shin-Osaka make practically a brief stop; when your train leaves Kyoto Station, please get prepared early to disembark.